Thank you Mr.justin<br><br><div class="gmail_quote">On Thu, Feb 21, 2008 at 9:50 PM, <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Re: Problem regarding tc_grps (Justin A. Lemkul)<br>
2. problem about position restrain (sudheer babu)<br>
3. Re: problem about position restrain (Justin A. Lemkul)<br>
4. Building Topology with all hydrogens (Subhrangshu Supakar)<br>
5. Re: Building Topology with all hydrogens (Justin A. Lemkul)<br>
6. Re: T-Coupling and COM removal (Markus Miettinen)<br>
7. CHARMM nonbonded parameters and grompp output (Justin A. Lemkul)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 21 Feb 2008 06:02:20 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Problem regarding tc_grps<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:1203591740.47bd5a3ca8997@webmail.vt.edu">1203591740.47bd5a3ca8997@webmail.vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Quoting sudheer babu <<a href="mailto:sudheer.pbm07@gmail.com">sudheer.pbm07@gmail.com</a>>:<br>
<br>
> Dear gmx-users,<br>
> I am working on membrane proteins, I have done position restrain step<br>
> successfully but, I have doubt about that tc_grps how to use? I have<br>
> searched in gmx-archives regrading this problem , but I found controversial<br>
> answers like 1.tc_grps - protein sol Cl<br>
> 2.<br>
> tc_grps - protein sol_Cl<br>
> 3.<br>
> tc_grps - protein Non-protein<br>
<br>
And, from the archives, you have undoubtedly seen many responses about which to<br>
use. Also have a look at:<br>
<br>
<a href="http://wiki.gromacs.org/index.php/Thermostats" target="_blank">http://wiki.gromacs.org/index.php/Thermostats</a><br>
<br>
-Justin<br>
<br>
> Thanks in advance.<br>
><br>
<br>
<br>
<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<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: 2<br>
Date: Thu, 21 Feb 2008 17:33:47 +0530<br>
From: "sudheer babu" <<a href="mailto:sudheer.pbm07@gmail.com">sudheer.pbm07@gmail.com</a>><br>
Subject: [gmx-users] problem about position restrain<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:76de29310802210403h80bac8bke6ed6a42c5668654@mail.gmail.com">76de29310802210403h80bac8bke6ed6a42c5668654@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi gmx users,<br>
I am trying to run position restrain step for protein embedded in popc. is<br>
it possible to do position restrain at a time for both popc and protein like<br>
below mentioned here?<br>
in " .top " file<br>
; Include Position restraint file<br>
#ifdef POSRES<br>
#include "lip_posre.itp"<br>
#include "posre.itp"<br>
#endif<br>
<br>
or any other way to do position restrain for both.<br>
pls help me.....<br>
Thanks in advance<br>
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Message: 3<br>
Date: Thu, 21 Feb 2008 07:27:33 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] problem about position restrain<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:1203596853.47bd6e355c11c@webmail.vt.edu">1203596853.47bd6e355c11c@webmail.vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Quoting sudheer babu <<a href="mailto:sudheer.pbm07@gmail.com">sudheer.pbm07@gmail.com</a>>:<br>
<br>
> Hi gmx users,<br>
> I am trying to run position restrain step for protein embedded in popc. is<br>
> it possible to do position restrain at a time for both popc and protein like<br>
> below mentioned here?<br>
> in " .top " file<br>
> ; Include Position restraint file<br>
> #ifdef POSRES<br>
> #include "lip_posre.itp"<br>
> #include "posre.itp"<br>
> #endif<br>
<br>
I don't know, have you tried it? Does it seem to work? Something that I have<br>
done before is the following:<br>
<br>
; position restrain protein<br>
#ifdef POSRES<br>
#include posre.itp<br>
#endif<br>
<br>
; position restrain lipid<br>
#ifdef POSRES_LIPID<br>
#include lipid_posre.itp<br>
#endif<br>
<br>
That way, you can define both, or only one throughout the course of minimization<br>
and equilibration, i.e.:<br>
<br>
define = -DPOSRES -DPOSRES_LIPID<br>
<br>
or<br>
<br>
define = -DPOSRES<br>
<br>
-Justin<br>
<br>
><br>
> or any other way to do position restrain for both.<br>
> pls help me.....<br>
> Thanks in advance<br>
><br>
<br>
<br>
<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<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: 4<br>
Date: Thu, 21 Feb 2008 17:50:14 +0530<br>
From: "Subhrangshu Supakar" <<a href="mailto:ssupakar@gmail.com">ssupakar@gmail.com</a>><br>
Subject: [gmx-users] Building Topology with all hydrogens<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:28ab3fc70802210420q65a6a757x78f23b7c30f028c1@mail.gmail.com">28ab3fc70802210420q65a6a757x78f23b7c30f028c1@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi All !<br>
I want to do a MD study of a few molecules in a box of sodium cetyl<br>
sulphate.<br>
I want the the topology Sod-cetyl-sulphate with all its hydrogens as without<br>
that there would occur a mismatch<br>
in the number of atoms in the system and the number of atoms in the topology<br>
file. I tried the the dundee server, but I got the topology of the molecule<br>
with no H.<br>
Can any one suggest a possible way for building the topology for the<br>
Sod-cetyl-sulphate with all its hydrogens.<br>
<br>
Subhrangshu Supakar<br>
Dept. of Bioinformatics<br>
WestBengal University of Technology<br>
Kolkkata, India<br>
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Message: 5<br>
Date: Thu, 21 Feb 2008 08:17:08 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Building Topology with all hydrogens<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:1203599828.47bd79d444753@webmail.vt.edu">1203599828.47bd79d444753@webmail.vt.edu</a>><br>
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<br>
Quoting Subhrangshu Supakar <<a href="mailto:ssupakar@gmail.com">ssupakar@gmail.com</a>>:<br>
<br>
> Hi All !<br>
> I want to do a MD study of a few molecules in a box of sodium cetyl<br>
> sulphate.<br>
> I want the the topology Sod-cetyl-sulphate with all its hydrogens as without<br>
> that there would occur a mismatch<br>
> in the number of atoms in the system and the number of atoms in the topology<br>
> file. I tried the the dundee server, but I got the topology of the molecule<br>
> with no H.<br>
> Can any one suggest a possible way for building the topology for the<br>
> Sod-cetyl-sulphate with all its hydrogens.<br>
<br>
You will have to derive the parameters yourself. See relevant discussions about<br>
ligands, drugs, etc. in the list archive (this sort of thing has been asked<br>
dozens of times in recent memory). Also have a look at:<br>
<br>
<a href="http://wiki.gromacs.org/index.php/Parameterization" target="_blank">http://wiki.gromacs.org/index.php/Parameterization</a><br>
<br>
<a href="http://wiki.gromacs.org/index.php/Exotic_Species" target="_blank">http://wiki.gromacs.org/index.php/Exotic_Species</a><br>
<br>
-Justin<br>
<br>
><br>
> Subhrangshu Supakar<br>
> Dept. of Bioinformatics<br>
> WestBengal University of Technology<br>
> Kolkkata, India<br>
><br>
<br>
<br>
<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<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: Thu, 21 Feb 2008 15:42:54 +0200<br>
From: Markus Miettinen <<a href="mailto:markus.miettinen@tkk.fi">markus.miettinen@tkk.fi</a>><br>
Subject: [gmx-users] Re: T-Coupling and COM removal<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:9D00BEE0-ECC2-4943-A9F4-7075EF20B0B3@tkk.fi">9D00BEE0-ECC2-4943-A9F4-7075EF20B0B3@tkk.fi</a>><br>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed<br>
<br>
On Feb 20, 2008, at 19:36 , <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:<br>
<br>
> Message: 4<br>
> Date: Wed, 20 Feb 2008 09:15:33 -0800<br>
> From: "Ilya Chorny" <<a href="mailto:ichorny@gmail.com">ichorny@gmail.com</a>><br>
> Subject: [gmx-users] T-Coupling and COM removal<br>
> To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> Message-ID:<br>
> <<a href="mailto:5f5f916d0802200915y1beff759ye244b11775355553@mail.gmail.com">5f5f916d0802200915y1beff759ye244b11775355553@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> HI All,<br>
><br>
> I ran some membrane protein simulations and got some strange<br>
> results. The<br>
> RMSD (~.18 nm) of the protein equilibrated quite nicely but when I<br>
> look at<br>
> the trajectory the protein seems to be diffusing way to much over<br>
> 20ns. The<br>
> protein has about 1000 AA. I calculated the KE of the protein,<br>
> lipid, and<br>
> water and got a KE that was 1.5RT, 1.2RT, and .8RT respectively.<br>
> My T is<br>
> 298K.<br>
> My COM removal and T-coupling is for the whole system. I am running<br>
> 3.3.1.<br>
> Is there a problem with T-coupling and COM removal on the whole<br>
> system?<br>
<br>
If you have set nstcomm=1, you should not experience a drift.<br>
<br>
For some reason, however, the center of mass of the whole simulation<br>
can slowly drift, even if explicit removal (nstcomm = 1) has been set.<br>
A Bugzilla has been posted, please see<br>
<br>
<a href="http://bugzilla.gromacs.org/show_bug.cgi?id=165" target="_blank">http://bugzilla.gromacs.org/show_bug.cgi?id=165</a><br>
<br>
for further details.<br>
<br>
<br>
Cheers,<br>
Markus Miettinen<br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Thu, 21 Feb 2008 11:19:44 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: [gmx-users] CHARMM nonbonded parameters and grompp output<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:1203610784.47bda4a013ba3@webmail.vt.edu">1203610784.47bda4a013ba3@webmail.vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
<br>
Hi all,<br>
<br>
As a number of others have attempted, I am exploring the use of the CHARMM force<br>
fields in Gromacs. I have read about a number of difficulties throughout the<br>
list archive, but I am seeing something that thusfar it seems no one has<br>
reported, regarding nonbonded parameters. Let me tell you what I've done so<br>
far, and perhaps someone can shed some light on what's going on.<br>
<br>
I downloaded the ffcharmm* files from the old User Contribution site, following<br>
a link I found in the archive. I created a .hdb file (for ease of use) and<br>
edited the .tdb files, as they contained some inconsistencies in atom naming<br>
and formatting. I converted the CHARMM27 force field parameters from Alex<br>
MacKerell's site using a script that was also made available through User<br>
Contributions, giving me ffcharmm.itp, ffcharmmbon.itp, and ffcharmmnb.itp. So<br>
far, so good. For the moment, I am also approximating the Urey-Bradley<br>
potential by using distance restraints, using scripts that came along with the<br>
ffcharmm package.<br>
<br>
I was able to produce a topology for hen egg white lysozyme (a decent system to<br>
test, I thought), with correct disulfides, charges, etc. and life was good. I<br>
ran grompp to attempt an in vacuo energy minimization, and saw this among my<br>
output:<br>
<br>
processing topology...<br>
Generated 0 of the 8646 non-bonded parameter combinations<br>
<br>
The rest of the grompp output indicated no errors or warnings (aside from a net<br>
charge, which is OK for now). I reasoned that there should be _some_ form of<br>
nonbonded interactions within the protein, correct? I read about 1-4<br>
interactions (i.e. OPLSAA generates these by scaling, so they are not<br>
explicitly included in ffoplsaanb.itp), but such scaling is reportedly not used<br>
in the CHARMM force field, and thus it was no surprise to find [ nonbond_params<br>
] within ffcharmmnb.itp. This brings me to my question: is grompp not finding<br>
these parameters? And if so, why?<br>
<br>
I noticed that ffcharmmnb.itp is formatted much like the GROMOS force field<br>
files (ffgmxnb.itp, ffG*nb.itp) and saw something that is not mentioned in the<br>
manual. The first line under [ atomtypes ] in each of the GROMOS force fields<br>
has formatting like:<br>
<br>
;name at.num mass charge ptype c6 c12<br>
O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06<br>
<br>
The at. num column is not mentioned in the manual (Gromacs version 3.3). Is it<br>
needed for proper interpretation of the *nb.itp files? Such a column is<br>
missing in my ffcharmmnb.itp file. The [ nonbond_params ] and [ pairtypes ]<br>
sections seem to have correct formatting, so I am not sure that this<br>
(potential) inconsistency among the [ atomtypes ] is causing the issue.<br>
<br>
Thanks for reading (yet another) long email from me, and thanks in advance if<br>
anyone has any ideas as to what's going on.<br>
<br>
-Justin<br>
<br>
<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<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>
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End of gmx-users Digest, Vol 46, Issue 67<br>
*****************************************<br>
</blockquote></div><br>