<div>Hi Justin, All, </div><div><br></div><div>This is my recent log of PDB2GMX command... I have got what I wanted but I would really appreciate if one you experts have a look and let me know weather everything is fine.</div>
<div><br></div><div>I have not calculated new charge distribution after removing the entries for H5T and H3T .. so here I have found non integral charges on molecule.. (which I am going to do right now).</div><div><br></div>
<div>Thanks Justin for your valuable suggestions.. :)</div><div><br></div><div>Thankfully</div><div>Raghav</div><div><br></div><div>Select the Force Field:</div><div>From current directory:</div><div> 1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)</div>
<div>From '/usr/local/gromacs/share/gromacs/top':</div><div> 2: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)</div><div> 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)</div>
<div> 4: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)</div><div> 5: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)</div><div> 6: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)</div>
<div> 7: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)</div><div> 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)</div><div> 9: CHARMM27 all-atom force field (with CMAP) - version 2.0</div>
<div>10: CHARMM36 all-atom force field (with CMAP)</div><div>11: GROMOS96 43a1 force field</div><div>12: GROMOS96 43a2 force field (improved alkane dihedrals)</div><div>13: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)</div>
<div>14: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)</div><div>15: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)</div><div>16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)</div><div>17: [DEPRECATED] Encad all-atom force field, using full solvent charges</div>
<div>18: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges</div><div>19: [DEPRECATED] Gromacs force field (see manual)</div><div>20: [DEPRECATED] Gromacs force field with hydrogens for NMR</div><div>
1</div><div><br></div><div>Using the Amber03 force field in directory ./amber03.ff</div><div><br></div><div>Opening force field file ./amber03.ff/watermodels.dat</div><div><br></div><div>Select the Water Model:</div><div>
1: TIP3P TIP 3-point, recommended</div><div> 2: TIP4P TIP 4-point</div><div> 3: TIP4P-Ew TIP 4-point optimized with Ewald</div><div> 4: SPC simple point charge</div><div> 5: SPC/E extended simple point charge</div>
<div> 6: None</div><div>1</div><div>Opening force field file ./amber03.ff/aminoacids.r2b</div><div>Opening force field file ./amber03.ff/dna.r2b</div><div>Opening force field file ./amber03.ff/rna.r2b</div><div>Reading test.pdb...</div>
<div>Read 'Good gRace! Old Maple Actually Chews Slate', 115 atoms</div><div>Analyzing pdb file</div><div>Splitting PDB chains based on TER records or changing chain id.</div><div>There are 1 chains and 0 blocks of water and 6 residues with 115 atoms</div>
<div><br></div><div> chain #res #atoms</div><div> 1 'A' 6 115 </div><div><br></div><div>All occupancies are one</div><div>Opening force field file ./amber03.ff/atomtypes.atp</div><div>Atomtype 1</div><div>
Reading residue database... (amber03)</div><div>Opening force field file ./amber03.ff/aminoacids.rtp</div><div>Residue 93</div><div>Sorting it all out...</div><div>Opening force field file ./amber03.ff/dna.rtp</div><div>Residue 110</div>
<div>Sorting it all out...</div><div>Opening force field file ./amber03.ff/rna.rtp</div><div>Residue 126</div><div>Sorting it all out...</div><div>Opening force field file ./amber03.ff/aminoacids.hdb</div><div>Opening force field file ./amber03.ff/dna.hdb</div>
<div>Opening force field file ./amber03.ff/rna.hdb</div><div>Opening force field file ./amber03.ff/aminoacids.n.tdb</div><div>Opening force field file ./amber03.ff/aminoacids.c.tdb</div><div><br></div><div>Back Off! I just backed up topol.top to ./#topol.top.21#</div>
<div>Processing chain 1 'A' (115 atoms, 6 residues)</div><div>There are 0 donors and 0 acceptors</div><div>There are 0 hydrogen bonds</div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Identified residue DT1 as a starting terminus.</span></div>
<div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Identified residue DC6 as a ending terminus.</span></div><div>8 out of 8 lines of specbond.dat converted successfully</div><div>Opening force field file ./amber03.ff/aminoacids.arn</div>
<div>Opening force field file ./amber03.ff/dna.arn</div><div>Opening force field file ./amber03.ff/rna.arn</div><div>Checking for duplicate atoms....</div><div>Now there are 6 residues with 182 atoms</div><div>Making bonds...</div>
<div><br></div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">WARNING: atom H3T is missing in residue DC 6 in the pdb file</span></div><div> You might need to add atom H3T to the hydrogen database of building block DC3</div>
<div> in the file dna.hdb (see the manual)</div><div><br></div><div>There were 1 missing atoms in molecule DNA_chain_A</div><div>Number of bonds was 192, now 192</div><div>Generating angles, dihedrals and pairs...</div>
<div>Before cleaning: 466 pairs</div><div>Before cleaning: 496 dihedrals</div><div>Keeping all generated dihedrals</div><div>Making cmap torsions...There are 496 dihedrals, 36 impropers, 345 angles</div><div> 448 pairs, 192 bonds and 0 virtual sites</div>
<div>Total mass 1744.076 a.m.u.</div><div><span class="Apple-style-span" style="background-color: rgb(255, 255, 51);">Total charge -6.268 e</span></div><div>Writing topology</div><div><br></div><div>Back Off! I just backed up posre.itp to ./#posre.itp.1#</div>
<div><br></div><div>Writing coordinate file...</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>--------- PLEASE NOTE ------------</div><div>You have successfully generated a topology from: test.pdb.</div>
<div>The Amber03 force field and the tip3p water model are used.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>--------- ETON ESAELP ------------</div><div><br></div><div>gcq#67: "The Wheels On the Bus Go Round and Round" (J. Richman)</div>
<div><br></div><br><div class="gmail_quote">On Fri, Jul 8, 2011 at 5:48 AM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Send gmx-users mailing list submissions to<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of gmx-users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Re: Using new atom types (Fabian Casteblanco)<br>
2. Re: Re: Using new atom types (Justin A. Lemkul)<br>
3. Re: gmx-users Digest, Vol 87, Issue 44 (raghav singh)<br>
4. want to remove H5T entry form HDB file / open terminal (P, O)<br>
for polymerization of i-motif (raghav singh)<br>
5. Re: want to remove H5T entry form HDB file / open terminal<br>
(P, O) for polymerization of i-motif (Justin A. Lemkul)<br>
6. Re: Solute potential energy (Mark Abraham)<br>
7. help (=?GBK?B?z/7Tog==?=)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 7 Jul 2011 17:32:24 -0400<br>
From: Fabian Casteblanco <<a href="mailto:fabian.casteblanco@gmail.com">fabian.casteblanco@gmail.com</a>><br>
Subject: [gmx-users] Re: Using new atom types<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:CAG3KNbj2A_eUwxrTgm4wcpuxu6hAW_LLVqW4N_VXqqMGf1xr9w@mail.gmail.com">CAG3KNbj2A_eUwxrTgm4wcpuxu6hAW_LLVqW4N_VXqqMGf1xr9w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Hello Justin,<br>
<br>
Thanks for your help.<br>
<br>
Your response:<br>
No, you need the [defaults] directive from the force field. If you<br>
want to make<br>
a completely custom entity, then build your own, although likely most of the<br>
highest-level force field files are going to be the same. You can always add a<br>
new [atomtypes] directive in a proper location in your topology.<br>
<br>
Comment: So you are saying I need to refer to the [defaults]<br>
directive so I need to include {#include "charmm27.ff/forcefield.itp"}<br>
on my topology file? Below is the [defaults] directive for CHARMM. I<br>
can simply add my...<br>
<br>
>> -CgenFFbon.itp (bonded, angle, dihedral parameters,etc)<br>
>> -CgenFFnb.itp (nonbonded LJ values)<br>
>> -CgenFF.atp (atom type file)<br>
<br>
to this section?<br>
<br>
****************************************************************<br>
* Charmm to Gromacs port writted by *<br>
* Par Bjelkmar, <a href="mailto:bjelkmar@cbr.su.se">bjelkmar@cbr.su.se</a> *<br>
* Alternative correspondance: *<br>
* Erik Lindahl, <a href="mailto:lindahl@cbr.su.se">lindahl@cbr.su.se</a> *<br>
****************************************************************<br>
<br>
<br>
#define _FF_CHARMM<br>
<br>
[ defaults ]<br>
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>
1 2 yes 1.0 1.0<br>
<br>
#include "ffcharmm27nb.itp"<br>
#include "ffcharmm27bon.itp"<br>
**???{ #include add new CgenFFbon.itp and CgenFFnb.itp here? }???** ?<br>
<br>
Or would I need to create one almost identical to this except<br>
replacing the old ffcharm27.itp with my new Cgen.itp files?<br>
<br>
<br>
<br>
This is my sample topology. Your last statement said I could add<br>
[atomtypes] to this section. So I can simply include the [defaults]<br>
directive but just add the Cgenffbon.itp and cCgenffnb.itp to this<br>
section here?<br>
<br>
;SAMPLE topology:<br>
;<br>
;<br>
; Include forcefield parameters<br>
#include "charmm27.ff/forcefield.itp"<br>
**???{ #include add new CgenFFbon.itp and CgenFFnb.itp here? }???** ?<br>
<br>
#include "drug.itp"<br>
<br>
[ system ]<br>
; Name<br>
DrugName<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
DDD 1<br>
<br>
<br>
<br>
Thanks again for your help. Greatly appreciated!!<br>
<br>
Fabian Casteblanco<br>
Rutgers University<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 07 Jul 2011 17:49:38 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Re: Using new atom types<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E1629F2.8010300@vt.edu">4E1629F2.8010300@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Fabian Casteblanco wrote:<br>
> Hello Justin,<br>
><br>
> Thanks for your help.<br>
><br>
> Your response:<br>
> No, you need the [defaults] directive from the force field. If you<br>
> want to make<br>
> a completely custom entity, then build your own, although likely most of the<br>
> highest-level force field files are going to be the same. You can always add a<br>
> new [atomtypes] directive in a proper location in your topology.<br>
><br>
> Comment: So you are saying I need to refer to the [defaults]<br>
> directive so I need to include {#include "charmm27.ff/forcefield.itp"}<br>
> on my topology file? Below is the [defaults] directive for CHARMM. I<br>
> can simply add my...<br>
><br>
>>> -CgenFFbon.itp (bonded, angle, dihedral parameters,etc)<br>
>>> -CgenFFnb.itp (nonbonded LJ values)<br>
>>> -CgenFF.atp (atom type file)<br>
><br>
> to this section?<br>
><br>
> ****************************************************************<br>
> * Charmm to Gromacs port writted by *<br>
> * Par Bjelkmar, <a href="mailto:bjelkmar@cbr.su.se">bjelkmar@cbr.su.se</a> *<br>
> * Alternative correspondance: *<br>
> * Erik Lindahl, <a href="mailto:lindahl@cbr.su.se">lindahl@cbr.su.se</a> *<br>
> ****************************************************************<br>
><br>
><br>
> #define _FF_CHARMM<br>
><br>
> [ defaults ]<br>
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>
> 1 2 yes 1.0 1.0<br>
><br>
> #include "ffcharmm27nb.itp"<br>
> #include "ffcharmm27bon.itp"<br>
> **???{ #include add new CgenFFbon.itp and CgenFFnb.itp here? }???** ?<br>
><br>
<br>
No, because the required directives would be out of order and grompp would fail<br>
with a fatal error.<br>
<br>
> Or would I need to create one almost identical to this except<br>
> replacing the old ffcharm27.itp with my new Cgen.itp files?<br>
><br>
><br>
<br>
That depends. If your CgenFF* files are completely independent of the CHARMM27<br>
force field files already built into Gromacs, then yes, you can build everything<br>
from scratch. If you need any of the parameters from the existing CHARMM27<br>
force field, then you have to include your new parameters.<br>
<br>
><br>
> This is my sample topology. Your last statement said I could add<br>
> [atomtypes] to this section. So I can simply include the [defaults]<br>
> directive but just add the Cgenffbon.itp and cCgenffnb.itp to this<br>
> section here?<br>
><br>
> ;SAMPLE topology:<br>
> ;<br>
> ;<br>
> ; Include forcefield parameters<br>
> #include "charmm27.ff/forcefield.itp"<br>
> **???{ #include add new CgenFFbon.itp and CgenFFnb.itp here? }???** ?<br>
><br>
<br>
No, this would have the same effect as above. What is weird here is that this<br>
.top uses version 4.5 naming, but the files above appear to be from the 4.0.x<br>
series. Mixing these will probably not work. Be sure to standardize the files<br>
you're using to be consistent with the expectations of the Gromacs version<br>
you're using.<br>
<br>
The bottom line is that you should have a thorough read of Chapter 5 of the<br>
manual to understand the contents of the topology, from the highest level (force<br>
field) down to the molecule level, in terms of both the required order of<br>
directives and contents thereof. If the CGenFF parameters do not depend on the<br>
existing implementation, then you're probably better off not messing with the<br>
existing files and just creating your own, styled after the existing force field.<br>
<br>
-Justin<br>
<br>
> #include "drug.itp"<br>
><br>
> [ system ]<br>
> ; Name<br>
> DrugName<br>
><br>
> [ molecules ]<br>
> ; Compound #mols<br>
> DDD 1<br>
><br>
><br>
><br>
> Thanks again for your help. Greatly appreciated!!<br>
><br>
> Fabian Casteblanco<br>
> Rutgers University<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 7 Jul 2011 17:52:11 -0400<br>
From: raghav singh <<a href="mailto:raghavbioinfo@gmail.com">raghavbioinfo@gmail.com</a>><br>
Subject: [gmx-users] Re: gmx-users Digest, Vol 87, Issue 44<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<CAHsfQvCy_T3c0-DXqVHqSRS8B2jx3Z8oExaY=qcmMj=<a href="mailto:CJWAqiQ@mail.gmail.com">CJWAqiQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Justin,<br>
<br>
Yeah I have to remove that H from the that position to make my P open to<br>
contact with the O atom of the next unit.<br>
..but if you make some precise suggestion that How can I remove that entry..<br>
because I have tried to remove the entry from .RTP and .HDB files and in<br>
that case it starts giving me error that H5T is not available in rtp and hdb<br>
entry.<br>
<br>
I am just getting crazy with this thing... I am creating tons of DATA but<br>
NOT even a single thing which I can say a CLOSE SOLUTION... the best I found<br>
what I have posted. :(<br>
<br>
Need some serious help.. Passed the files to MY PROFESSOR :)<br>
<br>
Raghav<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110707/8db74052/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110707/8db74052/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Thu, 7 Jul 2011 17:53:35 -0400<br>
From: raghav singh <<a href="mailto:raghavbioinfo@gmail.com">raghavbioinfo@gmail.com</a>><br>
Subject: [gmx-users] want to remove H5T entry form HDB file / open<br>
terminal (P, O) for polymerization of i-motif<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:CAHsfQvAO4Ra0ehrbjCj41iWwcc6y2_BFqRE5KaxhJofZ1xKbSQ@mail.gmail.com">CAHsfQvAO4Ra0ehrbjCj41iWwcc6y2_BFqRE5KaxhJofZ1xKbSQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Justin,<br>
<br>
Yeah I have to remove that H from the that position to make my P open to<br>
contact with the O atom of the next unit.<br>
..but if you make some precise suggestion that How can I remove that entry..<br>
because I have tried to remove the entry from .RTP and .HDB files and in<br>
that case it starts giving me error that H5T is not available in rtp and hdb<br>
entry.<br>
<br>
I am just getting crazy with this thing... I am creating tons of DATA but<br>
NOT even a single thing which I can say a CLOSE SOLUTION... the best I found<br>
what I have posted. :(<br>
<br>
Need some serious help.. Passed the files to MY PROFESSOR :)<br>
<br>
Raghav<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110707/1453c323/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110707/1453c323/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Thu, 07 Jul 2011 18:09:06 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] want to remove H5T entry form HDB file / open<br>
terminal (P, O) for polymerization of i-motif<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E162E82.9000600@vt.edu">4E162E82.9000600@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
raghav singh wrote:<br>
> Hi Justin,<br>
><br>
> Yeah I have to remove that H from the that position to make my P open to<br>
> contact with the O atom of the next unit.<br>
> ..but if you make some precise suggestion that How can I remove that<br>
> entry.. because I have tried to remove the entry from .RTP and .HDB<br>
> files and in that case it starts giving me error that H5T is not<br>
> available in rtp and hdb entry.<br>
<br>
You've not shown any evidence that anything you've tried should have even<br>
worked, for several reasons:<br>
<br>
1. Your .pdb file contains a residue named DT, but your .rtp entries have never<br>
matched that name. pdb2gmx will not match these entries if they do not have the<br>
same name.<br>
<br>
2. The .rtp and .hdb entries you've shown previously specify that H5T should be<br>
there, or otherwise built on. If you properly remove all references to H5T (and<br>
then consequently re-calculate the charges on the associated functional groups),<br>
then there is no way pdb2gmx will try to place the atom there. It simply can't.<br>
<br>
If you've gotten some error message, please copy and paste it rather than trying<br>
to interpret what you're seeing.<br>
<br>
><br>
> I am just getting crazy with this thing... I am creating tons of DATA<br>
> but NOT even a single thing which I can say a CLOSE SOLUTION... the best<br>
> I found what I have posted. :(<br>
><br>
> Need some serious help.. Passed the files to MY PROFESSOR :)<br>
><br>
<br>
I understand that everyone has urgent problems to solve, including the people<br>
trying to give of their time to help you. If you've gotten yourself in a bind,<br>
then I can't help that. You've not yet posted any evidence of anything that<br>
might actually accomplish your goal.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Fri, 08 Jul 2011 08:16:42 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Solute potential energy<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E16304A.6060101@anu.edu.au">4E16304A.6060101@anu.edu.au</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
On 8/07/2011 1:06 AM, Francesco Musiani wrote:<br>
> Dear Gromacs users,<br>
> I have the following problem: I need to calculate the potential energy<br>
> of a protein surrounded by explicit water.<br>
> In particular, I need to calculate the bond, angle, proper dihedral and<br>
> improper dihedral terms of potential energy for the solute protein only.<br>
> How can I extract this values from a trajectory?<br>
<br>
Cunning use of mdrun -rerun makes this fairly easy to achieve. Use<br>
trjconv and tpbconv to create subsets to rerun, IIRC. Search the<br>
archives for details.<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Fri, 8 Jul 2011 11:31:59 +0800 (CST)<br>
From: =?GBK?B?z/7Tog==?= <<a href="mailto:xiaoyingw11@163.com">xiaoyingw11@163.com</a>><br>
Subject: [gmx-users] help<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:5fbb45b0.12ca3.13107cd4a76.Coremail.xiaoyingw11@163.com">5fbb45b0.12ca3.13107cd4a76.Coremail.xiaoyingw11@163.com</a>><br>
Content-Type: text/plain; charset="gbk"<br>
<br>
Skipped content of type multipart/alternative-------------- next part --------------<br>
A non-text attachment was scrubbed...<br>
Name: md.mdp<br>
Type: application/octet-stream<br>
Size: 10428 bytes<br>
Desc: not available<br>
Url : <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110708/9d3db059/md.obj" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110708/9d3db059/md.obj</a><br>
<br>
------------------------------<br>
<font color="#888888"><br>
--<br>
gmx-users mailing list<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
<br>
End of gmx-users Digest, Vol 87, Issue 49<br>
*****************************************<br>
</font></blockquote></div><br>