Hello Justin.<br>Nice to hear from you.<br><br>I did the conversion of AMBER files to GROMACS type by the amb2gmx.pl found in the ffAMBER tools.<br><br>I used the command:<br>g_hbond -f input.pdb -s topol.tpr -n index.ndx -num hbnum.xvg -hbn hbond.ndx -hbm hbmap.xpm -r 0.4 <br>
<br>My input was a pdb file generated from the AMBER trajectory (mdcrd).<br><br>I checked the .gro file (onverted from AMBER) with gmxcheck, of which output is here I am pasting. Just have a look.<br><br>Checking file notty.gro<br>
Reading frames from gro file 'notty.gro created by rdparm2gmx.pl Fri Jul 11 17:38:48 IST 2008', 30261 atoms.<br>Reading frame 0 time 0.000<br># Atoms 30261<br>Precision 0.001 (nm)<br>Last frame 0 time 0.000<br>
<br>Item #frames Timestep (ps)<br>Step 0<br>Time 0<br>Lambda 0<br>Coords 1<br>Velocities 0<br>Forces 0<br>Box 1<br><br>Can you please suggest , what may be the possible error from this ?<br>
<br>BRM<br><br><br><br>gcq#254: "O My God, They Killed Kenny !" (South Park)<br><br><div class="gmail_quote">On Sun, Jul 13, 2008 at 12:19 PM, <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:<br>
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Today's Topics:<br>
<br>
1. error in g_hbond (Biswaranjan Meher)<br>
2. Re: Can GROMACS mutate a residue? (Lee Soin)<br>
3. Re: error in g_hbond (Justin A. Lemkul)<br>
4. PME User (Sang-Min Park)<br>
5. Re: PME User (David van der Spoel)<br>
6. gromacs bond type (prasun kumar)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sat, 12 Jul 2008 17:48:04 +0530<br>
From: "Biswaranjan Meher" <<a href="mailto:biswaranjan.meher@gmail.com">biswaranjan.meher@gmail.com</a>><br>
Subject: [gmx-users] error in g_hbond<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:b4c1302e0807120518p56d514cfpa98e69b521051c54@mail.gmail.com">b4c1302e0807120518p56d514cfpa98e69b521051c54@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear GROMACS users,<br>
I am new to gmx-users.<br>
<br>
I am analysing the H-bonding in my trajectory with the tool g_hbond.<br>
The trajectory was generated by the AMBER force fields.<br>
Now I have converted the AMBER prmtop and inpcrd files to GROMACS .top and<br>
.gro files.<br>
<br>
When I performed the g_hbond, I encountered with a fatal error<br>
<br>
Your computational box has shrunk too much.<br>
g_hbond can not handle this situation, sorry.<br>
<br>
Also I checked the postings in the archive related to this problem, but I<br>
didnt get the solution completely.<br>
So is it a problem of my AMBER traj./pdb files I am using or it some thing<br>
else.<br>
Can anyone will help me in this regard to get the solution ?<br>
<br>
Thanks in advance for your kind suggestions.<br>
<br>
BRM<br>
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Message: 2<br>
Date: Sat, 12 Jul 2008 20:44:45 +0800<br>
From: "Lee Soin" <<a href="mailto:nomadoro@gmail.com">nomadoro@gmail.com</a>><br>
Subject: Re: [gmx-users] Can GROMACS mutate a residue?<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:e2838e4e0807120544t2d8c0858g1949a805131ba436@mail.gmail.com">e2838e4e0807120544t2d8c0858g1949a805131ba436@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Thanks! And I've learned that Pymol can also do the job.<br>
<br>
2008/7/12 DEEPESH AGARWAL <<a href="mailto:deepesh.iitd@gmail.com">deepesh.iitd@gmail.com</a>>:<br>
<br>
> Hi,<br>
><br>
> In addition to what Justin has suggested, VMD has a tool to mutate a<br>
> residue- Extensions>Modeling>Mutate residue.<br>
><br>
> Deepesh<br>
><br>
><br>
> On 7/12/08, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
> ><br>
> ><br>
> > Lee Soin wrote:<br>
> >> Hi!<br>
> >> Is there a command in GROMACS that can substitute the atoms of a whole<br>
> >> residue for another? This is quite useful in doing mutation simulations.<br>
> >> Or if that's not possible, how should I mutate a residue? Thanks!<br>
> ><br>
> > I would use a program like DeepView (Swiss-PDBViewer), or maybe Modeller.<br>
> ><br>
> > -Justin<br>
> ><br>
> >><br>
> >> --<br>
> >> Sun Li<br>
> >> Department of Physics<br>
> >> Nanjing University, China<br>
> >><br>
> >><br>
> >> ------------------------------------------------------------------------<br>
> >><br>
> >> _______________________________________________<br>
> >> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> >> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> >> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
> posting!<br>
> >> Please don't post (un)subscribe requests to the list. Use the<br>
> >> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> >> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
> ><br>
> > --<br>
> > ========================================<br>
> ><br>
> > Justin A. Lemkul<br>
> > Graduate Research Assistant<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>
> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> > Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
> posting!<br>
> > Please don't post (un)subscribe requests to the list. Use the<br>
> > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> > Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
> ><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
<br>
<br>
<br>
--<br>
Sun Li<br>
Department of Physics<br>
Nanjing University, China<br>
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Message: 3<br>
Date: Sat, 12 Jul 2008 09:11:24 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] error in g_hbond<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:4878AD7C.8090504@vt.edu">4878AD7C.8090504@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Biswaranjan Meher wrote:<br>
> Dear GROMACS users,<br>
> I am new to gmx-users.<br>
><br>
> I am analysing the H-bonding in my trajectory with the tool g_hbond.<br>
> The trajectory was generated by the AMBER force fields.<br>
> Now I have converted the AMBER prmtop and inpcrd files to GROMACS .top<br>
> and .gro files.<br>
<br>
How did you do this conversion?<br>
<br>
><br>
> When I performed the g_hbond, I encountered with a fatal error<br>
<br>
What was the command you issued? Were you analyzing the .gro file, or some<br>
converted mdcrd file?<br>
<br>
><br>
> Your computational box has shrunk too much.<br>
> g_hbond can not handle this situation, sorry.<br>
><br>
> Also I checked the postings in the archive related to this problem, but<br>
> I didnt get the solution completely.<br>
> So is it a problem of my AMBER traj./pdb files I am using or it some<br>
> thing else.<br>
> Can anyone will help me in this regard to get the solution ?<br>
<br>
Use gmxcheck on whatever files you have tried to analyze to see if they contain<br>
the appropriate box vectors. I don't know how you did the conversion of the<br>
files from AMBER --> GROMACS, so that's a possible source of error.<br>
<br>
-Justin<br>
<br>
><br>
> Thanks in advance for your kind suggestions.<br>
><br>
> BRM<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<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, 12 Jul 2008 17:40:06 +0200<br>
From: Sang-Min Park <<a href="mailto:sanni@theochem.uni-frankfurt.de">sanni@theochem.uni-frankfurt.de</a>><br>
Subject: [gmx-users] PME User<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:200807121740.06885.sanni@theochem.uni-frankfurt.de">200807121740.06885.sanni@theochem.uni-frankfurt.de</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
<br>
Dear all,<br>
<br>
I read in <a href="http://www.gromacs.org/gromacs/revisions/" target="_blank">www.gromacs.org/gromacs/revisions/</a> in the report of<br>
David van der Spoel<br>
<br>
"Added support for a combination of PME and User determined coulomb<br>
potentials. The user has to take care that the combination of Coulomb and<br>
standard PME makes sense" ( 8 Feb. 2005)<br>
<br>
I don't understand what that means.<br>
<br>
As I know the Ewald Sum consist of the reciprocal and direct space term<br>
which are derivated for the f(x)=1/r function.<br>
<br>
In this sense I don't know what gromacs would do when I would specify<br>
PME-User with a potential that is different from f(x).<br>
<br>
1. Can someone explain me what gromacs is doing when one sets PME-User ? <br>
<br>
2. Furthermore I would like to know if the user defined potential tables are<br>
also used to calculate the long range interactions.<br>
<br>
Thank you for your time<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Sat, 12 Jul 2008 17:49:22 +0200<br>
From: David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-users] PME User<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:4878D282.3050501@xray.bmc.uu.se">4878D282.3050501@xray.bmc.uu.se</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Sang-Min Park wrote:<br>
> Dear all,<br>
><br>
> I read in <a href="http://www.gromacs.org/gromacs/revisions/" target="_blank">www.gromacs.org/gromacs/revisions/</a> in the report of<br>
> David van der Spoel<br>
><br>
> "Added support for a combination of PME and User determined coulomb<br>
> potentials. The user has to take care that the combination of Coulomb and<br>
> standard PME makes sense" ( 8 Feb. 2005)<br>
><br>
> I don't understand what that means.<br>
><br>
> As I know the Ewald Sum consist of the reciprocal and direct space term<br>
> which are derivated for the f(x)=1/r function.<br>
><br>
> In this sense I don't know what gromacs would do when I would specify<br>
> PME-User with a potential that is different from f(x).<br>
><br>
> 1. Can someone explain me what gromacs is doing when one sets PME-User ?<br>
<br>
Let's say you want to replace the Coulomb potential Fc(r) by your own<br>
Fuser(r). Then you have to subtract the Long Range part of the coulomb<br>
potential Fc(r,LR) from your F(r) in the short range potential to get<br>
the correct sum. Note that this also dependent on the cut-off, so if you<br>
decide to change the cut-off you need a new lookup table for the<br>
short-range.<br>
<br>
><br>
> 2. Furthermore I would like to know if the user defined potential tables are<br>
> also used to calculate the long range interactions.<br>
><br>
> Thank you for your time<br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
<br>
--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Sun, 13 Jul 2008 12:18:41 +0530<br>
From: "prasun kumar" <<a href="mailto:prasun30@gmail.com">prasun30@gmail.com</a>><br>
Subject: [gmx-users] gromacs bond type<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:a473abdb0807122348v52f1dcfcw5b4241794eabb536@mail.gmail.com">a473abdb0807122348v52f1dcfcw5b4241794eabb536@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
dear users,<br>
I am trying to get some information about the bond type,angle type and<br>
dihedral angle type.<br>
can any one please tell me what is the bond type of C-F.angle type for<br>
F-C-F,dihedral angle type of F-C-C-O &F-C-C-H.<br>
Or any one can tell me how to define the gromacs type for bonds,angles.I<br>
tried to read the 5th chapter but not getting any thing.<br>
actually i am lookig forward to include TFE in the rtp file for my<br>
simulation of peptide in TFE.<br>
Please help me.<br>
Thanx in advance<br>
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</blockquote></div><br>