Dear Mark/Justin,<br><br>Thanks for your suggestions. I think I now have a good understanding of what you are talking about. Please answer my one last query in connection with this. Can the NADPH molecule from the starting PDB file be made to comply with the entry for NADPH in Gromacs In built resiude topology file [ NDPP ]. The problem I see in this is that this topology had the explicit polar hydrogens which we do not have in the starting PDB file and even after renaming the atom names and the residue names in the PDB to match with this in built topologies it clearly gives a warning about the missing polar hydrogens. How does one use these inbuilt topologies? What is adviced in this case- Generate topologies some where else (like PRODRG and do the necessary fine tuning) and use them? (or) Can it be made to comply with the in built topology in someway? and finally can the same charges/charge groups as that of the inbuilt topology be assigned to the PRODRG topologies in hope any better better behavior of the system?<br>
<br><div class="gmail_quote">On Sun, Mar 27, 2011 at 8:01 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;">
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Today's Topics:<br>
<br>
1. Re: Re: Alcohol Dehydrogenase MD simulation....Reg<br>
(Justin A. Lemkul)<br>
2. mdrun cannot append to file larger than 2Gb (Warren Gallin)<br>
3. Re: mdrun cannot append to file larger than 2Gb (Justin A. Lemkul)<br>
4. Best Program for Simulating Lipid Bilayers in Water (Nancy)<br>
5. Re: Re: Alcohol Dehydrogenase MD simulation....Reg (Mark Abraham)<br>
6. RMSD Calculation (Nancy)<br>
7. Re: RMSD Calculation (Justin A. Lemkul)<br>
8. How can I convert Gromacs ouput to Desmond input file?? (???)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sat, 26 Mar 2011 13:53:31 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Re: Alcohol Dehydrogenase MD<br>
simulation....Reg<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:4D8E281B.5020202@vt.edu">4D8E281B.5020202@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
Please choose a relevant subject line and do not reply to the entire digest; it<br>
confuses the archive.<br>
<br>
Kishore wrote:<br>
> Dear Mark,<br>
><br>
> As you correctly pointed out, I had looked into those improper dihedral<br>
> specifications several times before and it seems that they are properly<br>
> mentioned in the .itp file. I have been using the topologies generated<br>
> by PRODRG server for NADPH as i could not make it comply with the<br>
> inbuilt residue template library topologies. In this topologies<br>
> generated by PRODRG there is a directive called [ dihedrals ] and it<br>
> listed out all the dihedrals with comment lines showing proper and<br>
> improper dihedrals, but this seems to differ from the way the the<br>
> topologies are defined in the gromacs inbuilt template library which<br>
> only lists out the impropers. Does this make any difference in terms of<br>
> grompp interpreting them during the preprocessing? I am herein pasting a<br>
> section of that dihedrals and a snapshot of the NADPH molecule with the<br>
> atom names labelled so that you can see that the impropers you mentioned<br>
> in your reply are infact mentioned in the .itp file I am using.<br>
><br>
<br>
Gromacs separates proper and improper dihedrals in [dihedrals] directives,<br>
presumably for convenience. Having one or two directives with proper contents<br>
does not make a difference. If, however, PRODRG is assigning parameters that<br>
the force field library does not, that just sounds like typical PRODRG behavior<br>
- its parameters are often incorrect and one has to know the proper way to<br>
handle re-assigning parameters. Bonded parameters are often more correct than<br>
charges and charge groups from PRODRG, which are wrong in all the cases I've<br>
ever seen.<br>
<br>
<a href="http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips" target="_blank">http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips</a><br>
<br>
-Justin<br>
<br>
> The three improper dihedrals you have mentioned are highlighted<br>
> below...please correct me in case if i am getting the meaning<br>
> wrong..Sorry for flooding with long posts, but I am in a great need for<br>
> some help on this.<br>
><br>
> [ dihedrals ]<br>
> ; ai aj ak al fu c0, c1, m, ...<br>
> 1 4 3 2 2 0.0 167.4 0.0 167.4 ; imp NBS<br>
> CBQ H8M HBS<br>
> 4 1 5 6 2 0.0 167.4 0.0 167.4 ; imp CBQ<br>
> NBS OBT CAV<br>
> 6 4 9 7 2 0.0 167.4 0.0 167.4 ; imp CAV<br>
> CBQ CBE CAN<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>
<br>
Message: 2<br>
Date: Sat, 26 Mar 2011 11:29:56 -0600<br>
From: Warren Gallin <<a href="mailto:wgallin@ualberta.ca">wgallin@ualberta.ca</a>><br>
Subject: [gmx-users] mdrun cannot append to file larger than 2Gb<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:E74D013E-F316-40E1-A78A-7D76EA345A52@ualberta.ca">E74D013E-F316-40E1-A78A-7D76EA345A52@ualberta.ca</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Hi,<br>
<br>
Using GROMACS 4.5.3 I tried to continue an mdrun from a checkpoint, and got an error that I have never seen before, to whit:<br>
<br>
Program mdrun_mpi, VERSION 4.5.3<br>
Source code file: /global/software/build/gromacs-4.5.3/gromacs/src/gmxlib/checkpoint.c, line: 1727<br>
<br>
Fatal error:<br>
The original run wrote a file called 'traj.xtc' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
<br>
<br>
I've never had a problem with extending runs like this before.<br>
<br>
As suggested, I then ran with -noappend set, and it ran fine, creating a new set of numbered files for the ouput. I am assuming that I'll be able to combine the trajectory files at the end of the process.<br>
<br>
Have I missed some fine point in compiling that has left mdrun a little broken?<br>
<br>
Thanks,<br>
<br>
Warren Gallin<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Sat, 26 Mar 2011 14:08:55 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] mdrun cannot append to file larger than 2Gb<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:4D8E2BB7.2020809@vt.edu">4D8E2BB7.2020809@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Warren Gallin wrote:<br>
> Hi,<br>
><br>
> Using GROMACS 4.5.3 I tried to continue an mdrun from a checkpoint, and got an error that I have never seen before, to whit:<br>
><br>
> Program mdrun_mpi, VERSION 4.5.3<br>
> Source code file: /global/software/build/gromacs-4.5.3/gromacs/src/gmxlib/checkpoint.c, line: 1727<br>
><br>
> Fatal error:<br>
> The original run wrote a file called 'traj.xtc' which is larger than 2 GB, but mdrun did not support large file offsets. Can not append. Run mdrun with -noappend<br>
> For more information and tips for troubleshooting, please check the GROMACS<br>
> website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
><br>
><br>
><br>
> I've never had a problem with extending runs like this before.<br>
><br>
> As suggested, I then ran with -noappend set, and it ran fine, creating a new set of numbered files for the ouput. I am assuming that I'll be able to combine the trajectory files at the end of the process.<br>
><br>
<br>
Correct.<br>
<br>
> Have I missed some fine point in compiling that has left mdrun a little broken?<br>
><br>
<br>
Possibly, but it probably depends more on your system's architecture than<br>
anything you did. There is a configure option --disable-largefile (which should<br>
be the default), so you'd have to check config.log to see if this was changed to<br>
--enable-largefile based on what the configuration script found. Or you can<br>
re-compile and see if configuration fails with --enable-largefile and understand<br>
the reason.<br>
<br>
-Justin<br>
<br>
> Thanks,<br>
><br>
> Warren Gallin--<br>
> gmx-users mailing list <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>
> Please don't post (un)subscribe requests to the list. Use the<br>
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><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: 4<br>
Date: Sat, 26 Mar 2011 14:18:26 -0400<br>
From: Nancy <<a href="mailto:nancy5villa@gmail.com">nancy5villa@gmail.com</a>><br>
Subject: [gmx-users] Best Program for Simulating Lipid Bilayers in<br>
Water<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<AANLkTi=<a href="mailto:VdXMMy0gSvmHEm669i_fr28EDbkrMd3Ei45PB@mail.gmail.com">VdXMMy0gSvmHEm669i_fr28EDbkrMd3Ei45PB@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi All,<br>
<br>
I heard that LAMMPS is supposedly good for simulating lipid bilayers in<br>
water. I haven't used LAMMPS before; does anyone know if it would be worth<br>
to try it in addition to Gromacs?<br>
<br>
Thanks in advance,<br>
Nancy<br>
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<br>
Message: 5<br>
Date: Sun, 27 Mar 2011 11:10:30 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Re: Alcohol Dehydrogenase MD<br>
simulation....Reg<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:4D8E8076.5070204@anu.edu.au">4D8E8076.5070204@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
><br>
> Kishore wrote:<br>
>> Dear Mark,<br>
>><br>
>> As you correctly pointed out, I had looked into those improper<br>
>> dihedral specifications several times before and it seems that they<br>
>> are properly mentioned in the .itp file. I have been using the<br>
>> topologies generated by PRODRG server for NADPH as i could not make<br>
>> it comply with the inbuilt residue template library topologies. In<br>
>> this topologies generated by PRODRG there is a directive called [<br>
>> dihedrals ] and it listed out all the dihedrals with comment lines<br>
>> showing proper and improper dihedrals, but this seems to differ from<br>
>> the way the the topologies are defined in the gromacs inbuilt<br>
>> template library which only lists out the impropers. Does this make<br>
>> any difference in terms of grompp interpreting them during the<br>
>> preprocessing? I am herein pasting a section of that dihedrals and a<br>
>> snapshot of the NADPH molecule with the atom names labelled so that<br>
>> you can see that the impropers you mentioned in your reply are infact<br>
>> mentioned in the .itp file I am using.<br>
>><br>
><br>
>> The three improper dihedrals you have mentioned are highlighted<br>
>> below...please correct me in case if i am getting the meaning<br>
>> wrong..Sorry for flooding with long posts, but I am in a great need<br>
>> for some help on this.<br>
>><br>
>> [ dihedrals ]<br>
>> ; ai aj ak al fu c0, c1, m, ...<br>
>> 1 4 3 2 2 0.0 167.4 0.0 167.4 ; imp NBS<br>
>> CBQ H8M HBS 4 1 5 6 2 0.0 167.4 0.0<br>
>> 167.4 ; imp CBQ NBS OBT CAV 6 4 9 7 2 0.0<br>
>> 167.4 0.0 167.4 ; imp CAV CBQ CBE CAN<br>
><br>
<br>
That looks like the correct function form on reasonable atoms - but<br>
you'd have to check the naming scheme yourself. Do the charges look<br>
reasonable to your chemical experience? How does a simulation of just<br>
NADPH in vacuo go? In a small water box?<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Sat, 26 Mar 2011 21:25:32 -0400<br>
From: Nancy <<a href="mailto:nancy5villa@gmail.com">nancy5villa@gmail.com</a>><br>
Subject: [gmx-users] RMSD Calculation<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<AANLkTi=<a href="mailto:AuVz3npG67d87AjLHPqRcqH2aumSg8GSbsnBg@mail.gmail.com">AuVz3npG67d87AjLHPqRcqH2aumSg8GSbsnBg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi All,<br>
<br>
I need to determine the RMSD of a small molecule cocrystallized ligand,<br>
against a large number of predicted docked conformations. Please let me<br>
know what is the best method for doing this.<br>
<br>
Thank you very much,<br>
Nancy<br>
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<br>
Message: 7<br>
Date: Sat, 26 Mar 2011 21:27:43 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] RMSD Calculation<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:4D8E928F.8030805@vt.edu">4D8E928F.8030805@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Nancy wrote:<br>
> Hi All,<br>
><br>
> I need to determine the RMSD of a small molecule cocrystallized ligand,<br>
> against a large number of predicted docked conformations. Please let me<br>
> know what is the best method for doing this.<br>
><br>
<br>
I answered this yesterday:<br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2011-March/059697.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-March/059697.html</a><br>
<br>
If there's some reason you can't get that to work, then don't simply re-post the<br>
same original question. Iterative calls to g_rms are quite straightforward to<br>
script.<br>
<br>
-Justin<br>
<br>
> Thank you very much,<br>
> Nancy<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>
<br>
Message: 8<br>
Date: Sun, 27 Mar 2011 02:18:49 +0000<br>
From: ??? <<a href="mailto:nammika@hotmail.com">nammika@hotmail.com</a>><br>
Subject: [gmx-users] How can I convert Gromacs ouput to Desmond input<br>
file??<br>
To: <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <COL117-W57B84C904AED3321E4C907A3BB0@phx.gbl><br>
Content-Type: text/plain; charset="ks_c_5601-1987"<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
Dear experts,<br>
<br>
Hi, I used to gromacs for MD, but there is need to make desmond file from gromacs output.<br>
<br>
If there is anyone who know how to this, please let me know.<br>
<br>
Thank you very much.<br>
<br>
-Hyun-<br>
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End of gmx-users Digest, Vol 83, Issue 188<br>
******************************************<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>KRISHNA KISHORE@IIT-MADRAS<br>