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! Andy
2009/3/5 <gmx-users-requ...@gromacs.org> > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. problem in running grompp (victor doss) > 2. problem running grompp - error message here (victor doss) > 3. Re: problem running grompp - error message here > (Justin A. Lemkul) > 4. OXY not found (Andy Torres) > 5. Re: OXY not found (Justin A. Lemkul) > 6. distance restraints for alpha helix (abhigna polavarapu) > 7. OXY not found (Chris Neale) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 5 Mar 2009 17:32:12 +0000 > From: victor doss <victordos...@hotmail.com> > Subject: [gmx-users] problem in running grompp > To: <gmx-users@gromacs.org> > Message-ID: <bay133-w1010815281df3ac24a8cc4d3...@phx.gbl> > Content-Type: text/plain; charset="windows-1252" > > > Hello, > > 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. > > Thanking you > > > Dr. Victor A. Doss > > > _________________________________________________________________ > The new Windows Live Messenger. You don’t want to miss this. > http://www.microsoft.com/india/windows/windowslive/messenger.aspx > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090305/07c26829/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 5 Mar 2009 17:34:59 +0000 > From: victor doss <victordos...@hotmail.com> > Subject: [gmx-users] problem running grompp - error message here > To: <gmx-users@gromacs.org> > Message-ID: <bay133-w324784eed131fbfb366f6bd3...@phx.gbl> > Content-Type: text/plain; charset="windows-1252" > > > Hello, > > 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. > > Thanking you > > > Dr. Victor A. Doss > > > processing topology... > Generated 332520 of the 332520 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 332520 of the 332520 1-4 parameter combinations > Excluding 3 bonded neighbours for Protein_A 1 > Excluding 2 bonded neighbours for SOL 82 > Excluding 2 bonded neighbours for SOL 9514 > NOTE: > System has non-zero total charge: 8.000000e+00 > > processing coordinates... > double-checking input for internal consistency... > > ------------------------------------------------------- > Program grompp, VERSION 3.3.3 > Source code file: ../../../../src/kernel/grompp.c, line: 1134 > > Fatal error: > There were 3 error(s) processing your input > ------------------------------------------------------- > > "Can't You Make This Thing Go Faster ?" (Black Crowes) > > d...@dv-laptop:~/g > > > _________________________________________________________________ > Twice the fun—Share photos while you chat with Windows Live Messenger. > http://www.microsoft.com/india/windows/windowslive/messenger.aspx > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090305/146dfa47/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Thu, 05 Mar 2009 13:02:29 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] problem running grompp - error message here > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <49b013b5.6030...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > victor doss wrote: > > Hello, > > > > 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. > > > > Thanking you > > > > > > Dr. Victor A. Doss > > > > > > processing topology... > > Generated 332520 of the 332520 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 0.5 > > Generated 332520 of the 332520 1-4 parameter combinations > > Excluding 3 bonded neighbours for Protein_A 1 > > Excluding 2 bonded neighbours for SOL 82 > > Excluding 2 bonded neighbours for SOL 9514 > > NOTE: > > System has non-zero total charge: 8.000000e+00 > > > > processing coordinates... > > double-checking input for internal consistency... > > > > ------------------------------------------------------- > > Program grompp, VERSION 3.3.3 > > Source code file: ../../../../src/kernel/grompp.c, line: 1134 > > > > Fatal error: > > There were 3 error(s) processing your input > > ------------------------------------------------------- > > > > "Can't You Make This Thing Go Faster ?" (Black Crowes) > > > > The error messages themselves are actually printed above in the grompp > output. > Those are what you need to solve. Search the list archive for the error > messages, as well as the wiki site. > > -Justin > > > d...@dv-laptop:~/g > > > > > > ------------------------------------------------------------------------ > > Twice the fun— Share photos while you chat with Windows Live Messenger. > > <http://www.microsoft.com/india/windows/windowslive/messenger.aspx> > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Thu, 5 Mar 2009 16:17:27 -0200 > From: Andy Torres <torand2...@gmail.com> > Subject: [gmx-users] OXY not found > To: gmx-users@gromacs.org > Message-ID: > <2d35fa4f0903051017q71288fb4l4d8b5d9f0e024...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on > myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got the > following > > Fatal error: > Residue 'OXY' not found in residue topology database > > I check the ff and I did not found the oxigen molecule. > I saw that somebody allready use this molecule in the mailing list: > > On Tue, 18 Jun 2002, Valentin Gogonea > > Is there a chance to contact him? > Is this molecule in any other ff? > How can I fix this? > How can I take the OXI and SO4 molecules out of my .pdb file without making > mistakes? > Hopping to be clear. > Thanks in advance > > Andy > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090305/e4eca4f1/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Thu, 05 Mar 2009 13:32:22 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] OXY not found > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <49b01ab6....@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Andy Torres wrote: > > Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on > > myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got > > the following > > > > Fatal error: > > Residue 'OXY' not found in residue topology database > > > > I check the ff and I did not found the oxigen molecule. > > I saw that somebody allready use this molecule in the mailing list: > > > > On Tue, 18 Jun 2002, Valentin Gogonea > > > > Is there a chance to contact him? > > If this individual still subscribes to this list after all these years, you > may > get a reply. > > > Is this molecule in any other ff? > > Not typically. The force fields included in Gromacs are generally designed > for > condensed-phase species like proteins, nucleic acids, and small organics. > > > How can I fix this? > > That depends on your definition of "fix." If you need to simulate > myoglobin > with oxygen bound, you may be in for the difficult (read: very advanced!) > topic > of parameterization: > > http://wiki.gromacs.org/index.php/Parameterization > > With special consideration of the fact that the oxygen is probably bound to > heme: > > http://wiki.gromacs.org/index.php/Exotic_Species > > > How can I take the OXI and SO4 molecules out of my .pdb file without > > making mistakes? > > That depends on your definition of "mistake." Whether or not these > molecules > are relevant to your dynamics is a decision only you can make. > > -Justin > > > Hopping to be clear. > > Thanks in advance > > > > Andy > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 6 > Date: Thu, 5 Mar 2009 13:41:50 -0500 > From: abhigna polavarapu <abhig...@gmail.com> > Subject: [gmx-users] distance restraints for alpha helix > To: gmx-users@gromacs.org > Message-ID: > <feabd7290903051041w207fbf65v2383126bc3c5e...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear all, > I am trying to rebuild the alpha helix of one the chains > which got destroyed during the simulation. I found that we can do that > by distance restraints. So my question what is a better way of > distance restraints i.e should I restrain the hydrogen bonds of the > helix or any particular bond distances. I was not clear when I read > the chapter 4 in manual, what type' should I use for this, are these > parameterized anywhere because the manual says type' should be 1 for > bonds but for hydrogen bonds it varies from 0-2. I found an exercise > by David van der Spoel > > http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2004/exercises/index_html > but could not access the files, so I was not clear what atoms did he > use for restraints. > > Thank you > abhigna > > > ------------------------------ > > Message: 7 > Date: Thu, 05 Mar 2009 13:58:18 -0500 > From: Chris Neale <chris.ne...@utoronto.ca> > Subject: [gmx-users] OXY not found > To: gmx-users@gromacs.org > Message-ID: <49b020ca.9010...@utoronto.ca> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Andy, > > I did some work on molecular oxygen back in 2006. There have been a few > requests for molecular oxygen parameters so I decided to > 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 > these parameters are appropriate for your simulations. > > Note that I went with an epsilon value that I converted myself from Fisher > and Lago (3.71000e-01) and considered > the value used by Marrink and Berendsen (3.63000e-01) to have been > incorrectly converted. However, we never did publish our > simulations so I can't give you a reference for that discrepancy, which, to > my knowledge, has not previously been reported. > > After modifying the files as I outline below, you will need to rename your > oxygen residue and atomic names to match and then it > should respond properly to a run through pdb2gmx. > > 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 > to do that then. I am leaving the instructions intact as I did it at the > time since that is easier for me. > > 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). > 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: > Al-Abdul-Wahid MS, Yu CH, Batruch I, Evanics F, Pomès R, Prosser RS. "A > combined NMR and molecular dynamics study of the transmembrane > solubility and diffusion rate profile of dioxygen in lipid bilayers." > Biochemistry. 2006 Sep 5;45(35):10719-28. > Although that paper utilized the values directly from Marrink and > Berendsen. > > > ## Add to ffX.atp: > ; Added by Chris Neale March 16 2006 based on > ; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983 > ; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738 > OOT 15.99940 ; O in nitro R-NO2 > > ## Add to ffX.rtp: > [ OTWO ] > ; Added by Chris Neale March 16 2005 based on > ; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983 > ; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738 > [ atoms ] > OOA OOT 0.00 0 > OOB OOT 0.00 0 > [ bonds ] > OOA OOB > > ## Add to ffXbon.itp > ; Added by Chris Neale March 16 2005 based on > ; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983 > ; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738 > [ bondtypes ] > ; i j func b0 kb > OOT OOT 1 0.10160 659840. > ;[ constrainttypes ] > ;[ angletypes ] > ;[ dihedraltypes ] > > ## Add to ffXnb.itp: > ; Added by Chris Neale March 16 2006 based on > ; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983 > ; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738 > ; name bond_type mass charge ptype sigma epsilon > OOT OOT 1 15.99940 0.000 A 3.09000e-01 > 3.71000e-01 > > Chris. > > > -- original message -- > > Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on > myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got the > following > > Fatal error: > Residue 'OXY' not found in residue topology database > > I check the ff and I did not found the oxigen molecule. > I saw that somebody allready use this molecule in the mailing list: > > On Tue, 18 Jun 2002, Valentin Gogonea > > Is there a chance to contact him? > Is this molecule in any other ff? > How can I fix this? > How can I take the OXI and SO4 molecules out of my .pdb file without making > mistakes? > Hopping to be clear. > Thanks in advance > > Andy > > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 59, Issue 51 > ***************************************** >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php