Thanks Justin and Chris for the fast answer! I follow the Chris instructions but modifying the molecule name '[ OTWO ]' for '[ OTW ]' because otherwise gromacs error appears (there are other names with 4 letters code, I don't know why these is not valid). But it's working now!<br>
Andy<br><br><div class="gmail_quote">2009/3/5 <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>></span><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. problem in running grompp (victor doss)<br>
2. problem running grompp - error message here (victor doss)<br>
3. Re: problem running grompp - error message here<br>
(Justin A. Lemkul)<br>
4. OXY not found (Andy Torres)<br>
5. Re: OXY not found (Justin A. Lemkul)<br>
6. distance restraints for alpha helix (abhigna polavarapu)<br>
7. OXY not found (Chris Neale)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 5 Mar 2009 17:32:12 +0000<br>
From: victor doss <<a href="mailto:victordoss64@hotmail.com" target="_blank">victordoss64@hotmail.com</a>><br>
Subject: [gmx-users] problem in running grompp<br>
To: <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <BAY133-W1010815281DF3AC24A8CC4D3A40@phx.gbl><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
<br>
Hello,<br>
<br>
when I run grompp I get the following error message always. Whoever has a correct fix to get rid of this error message and get the actual result, Please suggest.<br>
<br>
Thanking you<br>
<br>
<br>
Dr. Victor A. Doss<br>
<br>
<br>
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Message: 2<br>
Date: Thu, 5 Mar 2009 17:34:59 +0000<br>
From: victor doss <<a href="mailto:victordoss64@hotmail.com" target="_blank">victordoss64@hotmail.com</a>><br>
Subject: [gmx-users] problem running grompp - error message here<br>
To: <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <BAY133-W324784EED131FBFB366F6BD3A40@phx.gbl><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
<br>
Hello,<br>
<br>
when I run grompp I get the following error message<br>
always. Whoever has a correct fix to get rid of this error message and<br>
get the actual result, Please suggest.<br>
<br>
Thanking you<br>
<br>
<br>
Dr. Victor A. Doss<br>
<br>
<br>
processing topology...<br>
Generated 332520 of the 332520 non-bonded parameter combinations<br>
Generating 1-4 interactions: fudge = 0.5<br>
Generated 332520 of the 332520 1-4 parameter combinations<br>
Excluding 3 bonded neighbours for Protein_A 1<br>
Excluding 2 bonded neighbours for SOL 82<br>
Excluding 2 bonded neighbours for SOL 9514<br>
NOTE:<br>
System has non-zero total charge: 8.000000e+00<br>
<br>
processing coordinates...<br>
double-checking input for internal consistency...<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 3.3.3<br>
Source code file: ../../../../src/kernel/grompp.c, line: 1134<br>
<br>
Fatal error:<br>
There were 3 error(s) processing your input<br>
-------------------------------------------------------<br>
<br>
"Can't You Make This Thing Go Faster ?" (Black Crowes)<br>
<br>
dv@dv-laptop:~/g<br>
<br>
<br>
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Message: 3<br>
Date: Thu, 05 Mar 2009 13:02:29 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] problem running grompp - error message here<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:49B013B5.6030207@vt.edu" target="_blank">49B013B5.6030207@vt.edu</a>><br>
Content-Type: text/plain; charset=windows-1252; format=flowed<br>
<br>
<br>
<br>
victor doss wrote:<br>
> Hello,<br>
><br>
> when I run grompp I get the following error message always. Whoever<br>
> has a correct fix to get rid of this error message and get the actual<br>
> result, Please suggest.<br>
><br>
> Thanking you<br>
><br>
><br>
> Dr. Victor A. Doss<br>
><br>
><br>
> processing topology...<br>
> Generated 332520 of the 332520 non-bonded parameter combinations<br>
> Generating 1-4 interactions: fudge = 0.5<br>
> Generated 332520 of the 332520 1-4 parameter combinations<br>
> Excluding 3 bonded neighbours for Protein_A 1<br>
> Excluding 2 bonded neighbours for SOL 82<br>
> Excluding 2 bonded neighbours for SOL 9514<br>
> NOTE:<br>
> System has non-zero total charge: 8.000000e+00<br>
><br>
> processing coordinates...<br>
> double-checking input for internal consistency...<br>
><br>
> -------------------------------------------------------<br>
> Program grompp, VERSION 3.3.3<br>
> Source code file: ../../../../src/kernel/grompp.c, line: 1134<br>
><br>
> Fatal error:<br>
> There were 3 error(s) processing your input<br>
> -------------------------------------------------------<br>
><br>
> "Can't You Make This Thing Go Faster ?" (Black Crowes)<br>
><br>
<br>
The error messages themselves are actually printed above in the grompp output.<br>
Those are what you need to solve. Search the list archive for the error<br>
messages, as well as the wiki site.<br>
<br>
-Justin<br>
<br>
> dv@dv-laptop:~/g<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
> Twice the fun— Share photos while you chat with Windows Live Messenger.<br>
> <<a href="http://www.microsoft.com/india/windows/windowslive/messenger.aspx" target="_blank">http://www.microsoft.com/india/windows/windowslive/messenger.aspx</a>><br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
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> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
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> Please don't post (un)subscribe requests to the list. Use the<br>
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<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<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: Thu, 5 Mar 2009 16:17:27 -0200<br>
From: Andy Torres <<a href="mailto:torand2000@gmail.com" target="_blank">torand2000@gmail.com</a>><br>
Subject: [gmx-users] OXY not found<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:2d35fa4f0903051017q71288fb4l4d8b5d9f0e024ec8@mail.gmail.com" target="_blank">2d35fa4f0903051017q71288fb4l4d8b5d9f0e024ec8@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on<br>
myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got the<br>
following<br>
<br>
Fatal error:<br>
Residue 'OXY' not found in residue topology database<br>
<br>
I check the ff and I did not found the oxigen molecule.<br>
I saw that somebody allready use this molecule in the mailing list:<br>
<br>
On Tue, 18 Jun 2002, Valentin Gogonea<br>
<br>
Is there a chance to contact him?<br>
Is this molecule in any other ff?<br>
How can I fix this?<br>
How can I take the OXI and SO4 molecules out of my .pdb file without making<br>
mistakes?<br>
Hopping to be clear.<br>
Thanks in advance<br>
<br>
Andy<br>
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Message: 5<br>
Date: Thu, 05 Mar 2009 13:32:22 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] OXY not found<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:49B01AB6.905@vt.edu" target="_blank">49B01AB6.905@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Andy Torres wrote:<br>
> Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on<br>
> myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got<br>
> the following<br>
><br>
> Fatal error:<br>
> Residue 'OXY' not found in residue topology database<br>
><br>
> I check the ff and I did not found the oxigen molecule.<br>
> I saw that somebody allready use this molecule in the mailing list:<br>
><br>
> On Tue, 18 Jun 2002, Valentin Gogonea<br>
><br>
> Is there a chance to contact him?<br>
<br>
If this individual still subscribes to this list after all these years, you may<br>
get a reply.<br>
<br>
> Is this molecule in any other ff?<br>
<br>
Not typically. The force fields included in Gromacs are generally designed for<br>
condensed-phase species like proteins, nucleic acids, and small organics.<br>
<br>
> How can I fix this?<br>
<br>
That depends on your definition of "fix." If you need to simulate myoglobin<br>
with oxygen bound, you may be in for the difficult (read: very advanced!) topic<br>
of parameterization:<br>
<br>
<a href="http://wiki.gromacs.org/index.php/Parameterization" target="_blank">http://wiki.gromacs.org/index.php/Parameterization</a><br>
<br>
With special consideration of the fact that the oxygen is probably bound to heme:<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>
> How can I take the OXI and SO4 molecules out of my .pdb file without<br>
> making mistakes?<br>
<br>
That depends on your definition of "mistake." Whether or not these molecules<br>
are relevant to your dynamics is a decision only you can make.<br>
<br>
-Justin<br>
<br>
> Hopping to be clear.<br>
> Thanks in advance<br>
><br>
> Andy<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">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" target="_blank">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>
ICTAS Doctoral Scholar<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: 6<br>
Date: Thu, 5 Mar 2009 13:41:50 -0500<br>
From: abhigna polavarapu <<a href="mailto:abhignap@gmail.com" target="_blank">abhignap@gmail.com</a>><br>
Subject: [gmx-users] distance restraints for alpha helix<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:feabd7290903051041w207fbf65v2383126bc3c5e39d@mail.gmail.com" target="_blank">feabd7290903051041w207fbf65v2383126bc3c5e39d@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Dear all,<br>
I am trying to rebuild the alpha helix of one the chains<br>
which got destroyed during the simulation. I found that we can do that<br>
by distance restraints. So my question what is a better way of<br>
distance restraints i.e should I restrain the hydrogen bonds of the<br>
helix or any particular bond distances. I was not clear when I read<br>
the chapter 4 in manual, what type' should I use for this, are these<br>
parameterized anywhere because the manual says type' should be 1 for<br>
bonds but for hydrogen bonds it varies from 0-2. I found an exercise<br>
by David van der Spoel<br>
<a href="http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2004/exercises/index_html" target="_blank">http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2004/exercises/index_html</a><br>
but could not access the files, so I was not clear what atoms did he<br>
use for restraints.<br>
<br>
Thank you<br>
abhigna<br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Thu, 05 Mar 2009 13:58:18 -0500<br>
From: Chris Neale <<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a>><br>
Subject: [gmx-users] OXY not found<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:49B020CA.9010106@utoronto.ca" target="_blank">49B020CA.9010106@utoronto.ca</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Hi Andy,<br>
<br>
I did some work on molecular oxygen back in 2006. There have been a few requests for molecular oxygen parameters so I decided to<br>
dig them up. Here are the parameters that I used for that work. I leave it to you to read the relevant papers and decide if<br>
these parameters are appropriate for your simulations.<br>
<br>
Note that I went with an epsilon value that I converted myself from Fisher and Lago (3.71000e-01) and considered<br>
the value used by Marrink and Berendsen (3.63000e-01) to have been incorrectly converted. However, we never did publish our<br>
simulations so I can't give you a reference for that discrepancy, which, to my knowledge, has not previously been reported.<br>
<br>
After modifying the files as I outline below, you will need to rename your oxygen residue and atomic names to match and then it<br>
should respond properly to a run through pdb2gmx.<br>
<br>
It probably makes a lot more sense to create an otwo.itp file, but I did this in my early gromacs days and didn;t know how<br>
to do that then. I am leaving the instructions intact as I did it at the time since that is easier for me.<br>
<br>
For a separate set of parameters, you might look at Bembenek and Rice JCP vol 113 #6 p. 2354-9 and Bembenek JCP 124 (2006).<br>
I did not decide that the Fisher and Lago parameters were "better", I just picked them since they had previously been used in our lab:<br>
Al-Abdul-Wahid MS, Yu CH, Batruch I, Evanics F, Pomès R, Prosser RS. "A combined NMR and molecular dynamics study of the transmembrane<br>
solubility and diffusion rate profile of dioxygen in lipid bilayers." Biochemistry. 2006 Sep 5;45(35):10719-28.<br>
Although that paper utilized the values directly from Marrink and Berendsen.<br>
<br>
<br>
## Add to ffX.atp:<br>
; Added by Chris Neale March 16 2006 based on<br>
; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983<br>
; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738<br>
OOT 15.99940 ; O in nitro R-NO2<br>
<br>
## Add to ffX.rtp:<br>
[ OTWO ]<br>
; Added by Chris Neale March 16 2005 based on<br>
; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983<br>
; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738<br>
[ atoms ]<br>
OOA OOT 0.00 0<br>
OOB OOT 0.00 0<br>
[ bonds ]<br>
OOA OOB<br>
<br>
## Add to ffXbon.itp<br>
; Added by Chris Neale March 16 2005 based on<br>
; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983<br>
; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738<br>
[ bondtypes ]<br>
; i j func b0 kb<br>
OOT OOT 1 0.10160 659840.<br>
;[ constrainttypes ]<br>
;[ angletypes ]<br>
;[ dihedraltypes ]<br>
<br>
## Add to ffXnb.itp:<br>
; Added by Chris Neale March 16 2006 based on<br>
; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983<br>
; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738<br>
; name bond_type mass charge ptype sigma epsilon<br>
OOT OOT 1 15.99940 0.000 A 3.09000e-01 3.71000e-01<br>
<br>
Chris.<br>
<br>
<br>
-- original message --<br>
<br>
Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on<br>
myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got the<br>
following<br>
<br>
Fatal error:<br>
Residue 'OXY' not found in residue topology database<br>
<br>
I check the ff and I did not found the oxigen molecule.<br>
I saw that somebody allready use this molecule in the mailing list:<br>
<br>
On Tue, 18 Jun 2002, Valentin Gogonea<br>
<br>
Is there a chance to contact him?<br>
Is this molecule in any other ff?<br>
How can I fix this?<br>
How can I take the OXI and SO4 molecules out of my .pdb file without making<br>
mistakes?<br>
Hopping to be clear.<br>
Thanks in advance<br>
<br>
Andy<br>
<br>
<br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list<br>
<a href="mailto:gmx-users@gromacs.org" target="_blank">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>
<br>
End of gmx-users Digest, Vol 59, Issue 51<br>
*****************************************<br>
</blockquote></div><br>