hi justin, I accept with u that simulation will not complete in 3ns, but as iam trying simulation at 400k for the first time i just kept it for 3ns to see how it will be.<br>and for checking conformational changes i saved the structures for each 100ps from the trajectory (is it a correct procedure for that.....?) <br>
<br>and is it possible to give explanation for the parameters and forcefield that we need to fallow for higher temperature simulations......? <br><br><div class="gmail_quote">On Mon, Aug 29, 2011 at 7:24 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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<br>
Today's Topics:<br>
<br>
1. Re: OPLS-AA Unknown Atomtype (Justin A. Lemkul)<br>
2. Error found on grompp - energy minimization (ITHAYARAJA)<br>
3. Re: Error found on grompp - energy minimization (Mark Abraham)<br>
4. Re: gromacs question topologie (Justin A. Lemkul)<br>
5. Re: Difficulty building a topology for a synthetic, branched<br>
PEG-peptide molecule [SOLVED] (Pablo Englebienne)<br>
6. simulation at higher temperatures (arun kumar)<br>
7. Re: simulation at higher temperatures (Justin A. Lemkul)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 29 Aug 2011 06:41:32 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype<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:4E5B6CDC.8000103@vt.edu">4E5B6CDC.8000103@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Yao Yao wrote:<br>
> Hi Justin,<br>
><br>
> Thanks for your last reply. Now it seems that OPLS has known the<br>
> atomtypes after I added those CA1, ... to ffoplsaanb.itp,<br>
> but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp,<br>
> it still gives errors like,<br>
><br>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#<br>
> checking input for internal consistency...<br>
> processing topology...<br>
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp<br>
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp<br>
> Opening library file<br>
> /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp<br>
> Generated 338253 of the 338253 non-bonded parameter combinations<br>
> Generating 1-4 interactions: fudge = 0.5<br>
> Generated 338253 of the 338253 1-4 parameter combinations<br>
><br>
> ERROR 1 [file cro.top, line 37]:<br>
> No default Bond types<br>
><br>
><br>
> ERROR 2 [file cro.top, line 71]:<br>
> No default Angle types<br>
><br>
><br>
> ERROR 3 [file cro.top, line 72]:<br>
> No default Angle types<br>
><br>
><br>
> ERROR 4 [file cro.top, line 85]:<br>
> No default Angle types<br>
><br>
><br>
> ERROR 5 [file cro.top, line 91]:<br>
> No default Ryckaert-Bell. types<br>
><br>
><br>
> ERROR 6 [file cro.top, line 92]:<br>
> No default Ryckaert-Bell. types<br>
><br>
><br>
> ERROR 7 [file cro.top, line 93]:<br>
> No default Ryckaert-Bell. types<br>
><br>
><br>
> ERROR 8 [file cro.top, line 108]:<br>
> No default Ryckaert-Bell. types<br>
><br>
><br>
> ERROR 9 [file cro.top, line 112]:<br>
> No default Proper Dih. types<br>
><br>
><br>
> ERROR 10 [file cro.top, line 113]:<br>
> No default Proper Dih. types<br>
><br>
><br>
> ERROR 11 [file cro.top, line 114]:<br>
> No default Proper Dih. types<br>
><br>
> Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp<br>
> Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp<br>
> Excluding 3 bonded neighbours molecule type 'Protein'<br>
> Excluding 2 bonded neighbours molecule type 'SOL'<br>
> Excluding 2 bonded neighbours molecule type 'SOL'<br>
><br>
> NOTE 1 [file cro.top, line 142]:<br>
> System has non-zero total charge: -1.022478e+00<br>
><br>
><br>
<br>
This total charge suggests that your topology is badly broken.<br>
<br>
><br>
> processing coordinates...<br>
> double-checking input for internal consistency...<br>
> renumbering atomtypes...<br>
> converting bonded parameters...<br>
><br>
> There was 1 note<br>
><br>
> -------------------------------------------------------<br>
> Program grompp, VERSION 4.0.7<br>
> Source code file: grompp.c, line: 986<br>
><br>
> Fatal error:<br>
> There were 11 errors in input file(s)<br>
> -----------------------------------------------<br>
><br>
> I do double-check those bondtypes, angles, and interactions mentioned in<br>
> the errors, and I am pretty sure I have already declared those values in<br>
> the ffoplsaabon.itp.<br>
> Is there any other file I also need to mention those values?<br>
><br>
<br>
If these types were actually present in ffoplsaabon.itp, then you wouldn't get<br>
these errors. Double check again.<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> | (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: Mon, 29 Aug 2011 16:48:36 +0530<br>
From: ITHAYARAJA <<a href="mailto:ithayaraja@gmail.com">ithayaraja@gmail.com</a>><br>
Subject: [gmx-users] Error found on grompp - energy minimization<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<CA+kBMrN7Ok_-JctVNVTA8GA05g_dhzPo585GUuB_8Li=<a href="mailto:FhNWXQ@mail.gmail.com">FhNWXQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear sir,<br>
I struck with the following error when i perform energy minimization. I<br>
unable to understand what did it mean? please make me clear.<br>
<br>
So kindly do the needful.<br>
<br>
Fatal error:<br>
Atomtype CR1 not found<br>
<br>
--<br>
**<br>
Ithayaraja M,<br>
Research Scholar,<br>
Department of Bionformatics,<br>
Bharathiar University,<br>
Coimbatore 641 046,<br>
Tamil Nadu<br>
India<br>
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Message: 3<br>
Date: Mon, 29 Aug 2011 21:22:53 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Error found on grompp - energy minimization<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:4E5B768D.206@anu.edu.au">4E5B768D.206@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 29/08/2011 9:18 PM, ITHAYARAJA wrote:<br>
> Dear sir,<br>
> I struck with the following error when i perform energy minimization.<br>
> I unable to understand what did it mean? please make me clear.<br>
><br>
> So kindly do the needful.<br>
><br>
> Fatal error:<br>
> Atomtype CR1 not found<br>
<br>
One of your molecules is trying to use an atomtype that isn't defined in<br>
your force field. However we can't guess why without a lot more<br>
information. See <a href="http://www.gromacs.org/Support" target="_blank">http://www.gromacs.org/Support</a><br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Mon, 29 Aug 2011 08:49:18 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: [gmx-users] Re: gromacs question topologie<br>
To: Joschua Sterzenbach <<a href="mailto:joschua_s@yahoo.de">joschua_s@yahoo.de</a>>, Discussion list for<br>
GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E5B8ACE.8010609@vt.edu">4E5B8ACE.8010609@vt.edu</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
<br>
Please keep all Gromacs-related correspondence on the gmx-users list,<br>
particularly if the discussion was previously carried out there. I am not a<br>
private tutor.<br>
<br>
Joschua Sterzenbach wrote:<br>
> Hi<br>
><br>
> is in the coordinate file only the geometry of the molecule?<br>
><br>
<br>
Yes. Have a look at its contents - all you'll find in most common formats are<br>
the (x,y,z) coordinates of the named atoms.<br>
<br>
> I ask because I only have the geometry.<br>
><br>
> Do I get the topologie out of the geometry or from where comes it?<br>
><br>
<br>
Please do some basic tutorial material to understand the Gromacs workflow. For<br>
residue-based biomolecules like proteins and nucleic acids, use pdb2gmx. For<br>
other molecules, g_x2top can create basic topologies for a limited number of<br>
force fields and molecules. Otherwise, you'll have to obtain the topology by<br>
some other means. There are other programs on the User Contributions page of<br>
the Gromacs site that can produce topologies for arbitrary molecules.<br>
<br>
You haven't said yet what you're working with, so all I can do is venture guesses.<br>
<br>
-Justin<br>
<br>
> The questions corresponds to this:<br>
> <a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg43478.html" target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg43478.html</a><br>
><br>
> Thanks<br>
> Regards<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> | (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: 5<br>
Date: Mon, 29 Aug 2011 15:02:30 +0200<br>
From: Pablo Englebienne <<a href="mailto:p.englebienne@tue.nl">p.englebienne@tue.nl</a>><br>
Subject: [gmx-users] Re: Difficulty building a topology for a<br>
synthetic, branched PEG-peptide molecule [SOLVED]<br>
To: "<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E5B8DE6.5050901@tue.nl">4E5B8DE6.5050901@tue.nl</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
> That's a long bond. Does your reference length in specbond.dat suit it?<br>
> IIRC there should be some evidence in the output of the special bond<br>
> being formed if it actually is. If not, your symptoms are probably related<br>
Hi Mark, indeed, I think that was part of the problem. pdb2gmx indeed<br>
outputs a message when a specbond.dat rule is matched and a bond formed.<br>
<br>
In case it helps to someone else or for reference purposes, I finally<br>
managed to solve the issue.<br>
<br>
Some of the lessons I learned:<br>
- make sure that the residues/atoms in specbond.dat were correct (I had<br>
defined a number of residues for termini and mid-chain PEG and<br>
connectors, and I got them confused at some point, so not all of them<br>
were being recognized properly). The "dangling bond at at least one of<br>
the terminal ends" given by pdb2gmx is most likely due to this and/or<br>
the protonation state of the residues connecting the fragments<br>
- each fragment is assigned a different chain letter in the source PDB<br>
file; in my case, for a system like<br>
<br>
[N-(peptide1)-C]-[N-(PEG)-C]-[N-(peptide2)-Lys-C]<br>
|<br>
NZ<br>
|<br>
[C-(PEG)-N]-[C-(peptide3)-N]<br>
<br>
each fragment in square brackets is assigned a different chain name in<br>
[A-E] in the PDB file:<br>
<br>
ATOM 123 N ARG A 1 74.024 13.299 50.237 1.00<br>
0.00 N1+<br>
^<br>
- always list the atoms within a chain in an N-to-C direction. This<br>
means that the main branch is defined first, and then the branching<br>
point is defined in an N-to-C direction, even if it is counterintuitive<br>
by the way they are connected. specbond.dat takes good care of setting<br>
up the connection in all cases (as long as they are well defined...).<br>
- the PEG residues need to be defined as type "Other" in residues.dat<br>
- call pdb2gmx to manually assign the termini and Lys protonation states<br>
manually, and to merge the chains into a single molecule:<br>
<br>
pdb2gmx-ter -f substrate.pdb-chainsep interactive-lys<br>
<br>
-> the "internal" termini (i.e., the ones that are peptide termini but<br>
are connected to a PEG chain) need to be given a protonation state of<br>
"None", while the "real" termini can be assigned as charged or neutral,<br>
depending on the conditions<br>
<br>
> Oh, and well done for constructing a good question. You would likely not have gotten anywhere giving less detail :)<br>
Thanks, it actually helped putting everything in writing, as it pointed<br>
out the few things that I hadn't yet looked at in detail...<br>
<br>
Pablo Englebienne, PhD<br>
Dept. of Biomedical Engineering<br>
Dept. of Chemistry and Chemical Engineering<br>
Institute for Complex Molecular Systems (ICMS)<br>
Eindhoven University of Technology, TU/e<br>
PO Box 513, HG -1.26<br>
5600 MB Eindhoven, The Netherlands<br>
Tel +31 40 247 5349<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Mon, 29 Aug 2011 19:19:36 +0530<br>
From: arun kumar <<a href="mailto:arunjones.kumar89@gmail.com">arunjones.kumar89@gmail.com</a>><br>
Subject: [gmx-users] simulation at higher temperatures<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<CAGM9vJ_iBDbQpnEkTdKYQyu2kaAz1Gqb3wL-UYv_06Lj=<a href="mailto:beh0w@mail.gmail.com">beh0w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi friends,<br>
<br>
As a part of my work i have to do simulation at higher temperature (400K or<br>
more) to study the folding, unfolding and stability of protein, for that i<br>
kept simulation for 3ns at 400k (400k temperature both in equilibration and<br>
production) keeping all the other parameters as usual (time step 2fs,<br>
explicit solvent model SPC, equilibration with NVT and NPT ensembles for<br>
100ps each ). the simulation was completed but ,<br>
1. in trajectory i found that protein is comming out of the box (cubic box<br>
-d 1.0) i think may be the box size was not sufficient (and i know that<br>
when we increase the temperature the velocity of atoms will increase).<br>
2. when i save the structure with minimum energy and saw in pymol i found<br>
the side chains, hydrogens was broken through out the protein.<br>
3. later i used the command ( trajconv -s md.tpr -f md.trr -o protein.pdb<br>
-pbc nojump -dt 10 ) to save the conformations at each 10 ps and to see the<br>
conformational changes by playing it as a movie in pymol , but i found a<br>
single conformation was just shaking through out the movie (this is<br>
happening in normal simulation also)<br>
<br>
later i read in gmx user problems that most of the force field parameters<br>
are calculated at room temperature, so in that case what are the parameters<br>
and forcefield that we need to fallow for higher temperature simulations.<br>
<br>
so can any one please takes time to explain this, it would be helpful for me<br>
to study further.<br>
<br>
Thanking you.<br>
<br>
with regards<br>
--<br>
Arun Kumar Somavarapu<br>
Center for Bioinformatics<br>
Pondicherry University<br>
Kalapet<br>
Puducherry-605014<br>
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Message: 7<br>
Date: Mon, 29 Aug 2011 09:53:45 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] simulation at higher temperatures<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:4E5B99E9.7060504@vt.edu">4E5B99E9.7060504@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
arun kumar wrote:<br>
><br>
> Hi friends,<br>
><br>
> As a part of my work i have to do simulation at higher temperature (400K<br>
> or more) to study the folding, unfolding and stability of protein, for<br>
> that i kept simulation for 3ns at 400k (400k temperature both in<br>
> equilibration and production) keeping all the other parameters as usual<br>
> (time step 2fs, explicit solvent model SPC, equilibration with NVT and<br>
> NPT ensembles for 100ps each ). the simulation was completed but ,<br>
<br>
I doubt any simulation, even of the simplest protein, is "complete" at 3 ns.<br>
<br>
> 1. in trajectory i found that protein is comming out of the box (cubic<br>
> box -d 1.0) i think may be the box size was not sufficient (and i know<br>
> that when we increase the temperature the velocity of atoms will increase).<br>
<br>
Please see FAQ #3 under the following section:<br>
<br>
<a href="http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization" target="_blank">http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization</a><br>
<br>
> 2. when i save the structure with minimum energy and saw in pymol i<br>
> found the side chains, hydrogens was broken through out the protein.<br>
<br>
Same as above.<br>
<br>
> 3. later i used the command ( trajconv -s md.tpr -f md.trr -o<br>
> protein.pdb -pbc nojump -dt 10 ) to save the conformations at each 10 ps<br>
> and to see the conformational changes by playing it as a movie in pymol<br>
> , but i found a single conformation was just shaking through out the<br>
> movie (this is happening in normal simulation also)<br>
<br>
Your simulation length is inadequate to view any conformational changes. These<br>
types of motions can require hundreds of ns, if not more (depending on the size<br>
of the protein), to visualize.<br>
<br>
-Justin<br>
<br>
><br>
> later i read in gmx user problems that most of the force field<br>
> parameters are calculated at room temperature, so in that case what are<br>
> the parameters and forcefield that we need to fallow for higher<br>
> temperature simulations.<br>
><br>
> so can any one please takes time to explain this, it would be helpful<br>
> for me to study further.<br>
><br>
> Thanking you.<br>
><br>
> with regards<br>
> --<br>
> Arun Kumar Somavarapu<br>
> Center for Bioinformatics<br>
> Pondicherry University<br>
> Kalapet<br>
> Puducherry-605014<br>
><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> | (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>
<font color="#888888"><br>
--<br>
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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 88, Issue 167<br>
******************************************<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Arun Kumar Somavarapu<div>Center for Bioinformatics</div><div>Pondicherry University</div><div>Kalapet</div><div>Puducherry-605014</div><br>