RE: [gmx-users] .n2t file for the CHARMM forcefield
Understandable. I meant the content of the .n2t file itself ; will it contain the same info as the OPLSAA with just changes in values according to the CHARMM field? Thank you Elie > Date: Wed, 10 Oct 2012 23:13:34 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] .n2t file for the CHARMM forcefield > > > > On 10/10/12 11:11 PM, Elie M wrote: > > > > Ok. This means that I have to form the .n2t file for the CHARMM field as it > > is required by x2top. For the OPLSAA field the format was: > > "Copls_1570.000 12.011 4H 0.108 H 0.108 H 0.108 C > > 0.150Copls_1580.000 12.0114H 0.108 H 0.108 C 0.150 > > C 0.150" > > How does this become in CHARMM? Shall we keep the atom names and change the > > oplsaa into atom types like CE1, CD,.and keep the rest fixed? > > > > The charges will be different and perhaps the bond lengths will be different. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] .n2t file for the CHARMM forcefield
Ok. This means that I have to form the .n2t file for the CHARMM field as it is required by x2top. For the OPLSAA field the format was: "Copls_1570.000 12.011 4H 0.108 H 0.108 H 0.108 C 0.150C opls_1580.000 12.0114H 0.108 H 0.108 C 0.150 C 0.150" How does this become in CHARMM? Shall we keep the atom names and change the oplsaa into atom types like CE1, CD,.and keep the rest fixed? Elie > Date: Wed, 10 Oct 2012 22:37:58 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] .n2t file for the CHARMM forcefield > > > > On 10/10/12 10:35 PM, Elie M wrote: > > > > Dear all, > > Is the form of the .n2t file (read by x2top to produce the top file) the > > same for all forcefields? I am using the CHARMM forcefield but I could not > > find an ffcharmm27.n2t file. > > The .n2t format is universal. Most force fields do not have .n2t files. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] .n2t file for the CHARMM forcefield
Dear all, Is the form of the .n2t file (read by x2top to produce the top file) the same for all forcefields? I am using the CHARMM forcefield but I could not find an ffcharmm27.n2t file. Regards Elie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] RB parameters for the OPLSAA force field.
Dear all, Does anyone know where I can find reference of how to calculate the RB parameters (C0-C5) for proper dihedrals? I have got some undefined dihedrals in my top file and I am not sure where to start. What kind of information do i need to calculate those parameters? any package that does that? Thanks Elie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Error with "grompp"
Yeah sorry about that. i thought about it at the moment I was sending the e-mail..The problem I am so desperate about getting all files correct to minimize my polymer. It has really taken a long time. Anyhow you were right. Switching the order did not do anything; the error is still there. Now it is a bit weird because the bond is there in the file then why it cannot find it? Any suggestions? Elie > Date: Sat, 6 Oct 2012 13:59:10 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/6/12 1:57 PM, Elie M wrote: > > > > Yes I just saw that. thanks for turning my attention. The top file assigned > > this order of the atomsdo you think switching the order of the atoms in > > the top file would solve the problem? > > In principle, I don't think it should matter, but it's something you can > check > yourself in less time than it takes to send an email :) > > -Justin > > > Elie > > > >> Date: Sat, 6 Oct 2012 13:26:38 -0400 > >> From: jalem...@vt.edu > >> To: gmx-users@gromacs.org > >> Subject: Re: [gmx-users] Error with "grompp" > >> > >> > >> > >> On 10/6/12 1:18 PM, Elie M wrote: > >>> > >>> This is what I did. For example one of the [bonds] problems is a bond > >>> between S and one of the carbons C in the thiophene molecule. In the n2t > >>> file. I have added OPLSA_734 S because it si related to " all-atom S: > >>> thiophenol (HS is #204)"; the corresponding C was assigned an OPLSA_735 I > >>> have looked for the symbols for these two: the first is SH and the other > >>> is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: > >>> SHCA 10.15925 186649.5 ; > >>> However the error related to this bond is still present. I was just > >>> thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen > >>> because the symbol is SH?? maybe this is the source of the error and I > >>> have to redefine things in the .n2t file? > >>> > >> > >> It may be a matter of the order of the atoms. SH is indeed sulfur (you > >> can tell > >> by the mass in atomtypes.atp and the fact that the first letter is S). The > >> corresponding H atom is HS, so that's not the problem. The parameters for > >> this > >> bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a > >> pre-4.5 > >> version): > >> > >> CASH 10.17400 209200.0 ; wlj > >> > >> -Justin > >> > >> -- > >> > >> > >> Justin A. Lemkul, Ph.D. > >> Research Scientist > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) 231-9080 > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >> > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Error with "grompp"
Yes I just saw that. thanks for turning my attention. The top file assigned this order of the atomsdo you think switching the order of the atoms in the top file would solve the problem? Elie > Date: Sat, 6 Oct 2012 13:26:38 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/6/12 1:18 PM, Elie M wrote: > > > > This is what I did. For example one of the [bonds] problems is a bond > > between S and one of the carbons C in the thiophene molecule. In the n2t > > file. I have added OPLSA_734 S because it si related to " all-atom S: > > thiophenol (HS is #204)"; the corresponding C was assigned an OPLSA_735 I > > have looked for the symbols for these two: the first is SH and the other is > > CA so in [bondtypes] in ffoplsaabon.itp I have added a line: > > SHCA 10.15925 186649.5 ; > > However the error related to this bond is still present. I was just > > thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen > > because the symbol is SH?? maybe this is the source of the error and I have > > to redefine things in the .n2t file? > > > > It may be a matter of the order of the atoms. SH is indeed sulfur (you can > tell > by the mass in atomtypes.atp and the fact that the first letter is S). The > corresponding H atom is HS, so that's not the problem. The parameters for > this > bond are already in ffbonded.itp (ffoplsaabon.itp in your case, with a > pre-4.5 > version): > >CASH 10.17400 209200.0 ; wlj > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Error with "grompp"
This is what I did. For example one of the [bonds] problems is a bond between S and one of the carbons C in the thiophene molecule. In the n2t file. I have added OPLSA_734 S because it si related to " all-atom S: thiophenol (HS is #204)"; the corresponding C was assigned an OPLSA_735 I have looked for the symbols for these two: the first is SH and the other is CA so in [bondtypes] in ffoplsaabon.itp I have added a line: SHCA 10.15925 186649.5 ; However the error related to this bond is still present. I was just thinking mabye that OPLSAA_734 for S is sulfur connected to Hydrogen because the symbol is SH?? maybe this is the source of the error and I have to redefine things in the .n2t file? Elie > Date: Fri, 5 Oct 2012 13:06:34 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/5/12 1:00 PM, Elie M wrote: > > > > I was able to find reasonable values of kb and b0 and inserted the info > > into foplsaabon.itp. I am still getting an error; what I did is the > > following: > > 1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I > > check the section [atomtypes] in fftoplsaa.nb and see to what symbol the > > oplsa_xxx corresponds for example (OW). If the problem was in the [bonds] > > directive, I plug the info there with the corresponding values of bo and kb > > and according to the format there, and I save. > > 3- i run grompp again but in vain as I still get the same number of errors > > (as I expect they should decrease in number if things were fixed). > > Am I still missing something that i should have done apart from filling in > > the numbers in ffoplsaabon.itp? > > > > Whatever changes you made were apparently ineffectual. You need to make sure > that you are adding parameters in the correct directives (i.e. bonds in > [bondtypes], angles in [angletypes], etc). Without seeing exactly what > you've > done, all I can say is that whatever you did wasn't correct. The approach is > theoretically sound, though. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Error with "grompp"
I was able to find reasonable values of kb and b0 and inserted the info into foplsaabon.itp. I am still getting an error; what I did is the following: 1- I went to ffoplsaa.n2t to check the OPLSA_XXX of the atoms.2- Next I check the section [atomtypes] in fftoplsaa.nb and see to what symbol the oplsa_xxx corresponds for example (OW). If the problem was in the [bonds] directive, I plug the info there with the corresponding values of bo and kb and according to the format there, and I save. 3- i run grompp again but in vain as I still get the same number of errors (as I expect they should decrease in number if things were fixed). Am I still missing something that i should have done apart from filling in the numbers in ffoplsaabon.itp? Thanks Elie > Date: Thu, 4 Oct 2012 21:25:29 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/4/12 5:56 PM, Elie M wrote: > > > > I guess the first parameter of each pair is easy to find. what about kb? k > > theta?. kb is the force constant isnt it? any reference about a method > > how to calculate them please? pr anything atht might be of help. > > > > Bonded parameters are generally based on vibrational spectra and X-ray data. > For OPLS, the bonded parameters were originally taken from an AMBER parameter > set in the mid-1980's and have some terms have subsequently been revised over > time. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Error with "grompp"
I guess the first parameter of each pair is easy to find. what about kb? k theta?. kb is the force constant isnt it? any reference about a method how to calculate them please? pr anything atht might be of help. Elie > Date: Thu, 4 Oct 2012 16:25:35 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/4/12 4:22 PM, Elie M wrote: > > > > I guess now I get what is happening finally. Correct me if I am wrong. The > > .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which > > was also modified to include atoms that were not there *but present in > > atomtypes.atp). The .top file describes all the bonds and angles in the > > molecule. This was successful. However the characteristics of some of those > > bonds are not described in the foplssabon.itp file; for example I have > > Sulfur > > in my molecule connected to carbon which has no entry in foplsaabon.itp and > > must be added to that file manually. I guess now I am in a position to check > > those bonds and add the relevant information which i will gather maybe from > > HYPERCHEM or ARGUSLAB??A final question is in order here: what do the > > You will have to calculate reasonable values in some way, yes. > > > parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and > > in what units? > > > > All of this is in the manual. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Error with "grompp"
I guess now I get what is happening finally. Correct me if I am wrong. The .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which was also modified to include atoms that were not there *but present in atomtypes.atp). The .top file describes all the bonds and angles in the molecule. This was successful. However the characteristics of some of those bonds are not described in the foplssabon.itp file; for example I have Sulfur in my molecule connected to carbon which has no entry in foplsaabon.itp and must be added to that file manually. I guess now I am in a position to check those bonds and add the relevant information which i will gather maybe from HYPERCHEM or ARGUSLAB??A final question is in order here: what do the parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and in what units? Thank you very much Elie > Date: Thu, 4 Oct 2012 12:25:48 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/4/12 12:13 PM, Elie M wrote: > > > > Thanks a lot. I have sorted out the error that occured in the > > ffoplsaabon.itp; I have commented ";" one line which was given the first > > two errors. Now the only errors remaining are the bonds, angles and some > > others. How to correct these? > > For example one of them is (the error occuring at line 118 which is no > > different from others). > > 111 [ bonds ] 112 ; aiaj functc0c1 > > c2c3 113 1 2 1 114 1 5 1 > > 115 147 1 116 2 3 1 117 248 1 > > 118 3 4 1 > > How can the source of error be known and corrected? > > The error message means that no suitable parameters exist in the force field > for > the bond that occurs between those atoms. You either need to parameterize > the > problematic bond(s) yourself or obtain parameters from some other reliable > source. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Error with "grompp"
Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; I have commented ";" one line which was given the first two errors. Now the only errors remaining are the bonds, angles and some others. How to correct these? For example one of them is (the error occuring at line 118 which is no different from others). 111 [ bonds ] 112 ; aiaj functc0c1 c2c3 113 1 2 1 114 1 5 1 115 1 47 1 116 2 3 1 117 248 1 118 3 4 1 How can the source of error be known and corrected? Elie > Date: Thu, 4 Oct 2012 10:26:04 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/4/12 10:12 AM, Elie M wrote: > > > > Hello everyone, > > Justin, I have repeated the procedures without doing any changes and it > > does seem that you were right about the broken file. However now I get a > > different set of errors: > > (1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of > > atomtypes for dihedral (4 instead of 2 or 4) > > > > > > > > (2) ERROR 2 [file ffoplsaabon.itp, line 2694]: Not enough parameters > > You should inspect ffoplsaabon.itp to see what is on these lines. It is odd > that grompp would complain about standard force field files if they have not > been changed. > > > and then a lot of errors of the type: > > > > ERROR 3 [file S54.top, line 118]: No default Bond types > > > > ERROR 4 [file S54.top, line 120]: No default Bond types > > > > ERROR 5 [file S54.top, line 124]: No default Bond types > > > > ERROR 6 [file S54.top, line 127]: No default Bond types... > > Maybe the main question is for the third error is how to define these bond > > types and angles? > > If a certain interaction is not available in ffbonded.itp (i.e. you've got > bonds > that are not parameterized in the chosen force field) you need to add them > either in ffbonded.itp (potentially dangerous, given the previous posts) or > directly in the topology (probably safer). > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Error with "grompp"
Hello everyone, Justin, I have repeated the procedures without doing any changes and it does seem that you were right about the broken file. However now I get a different set of errors: (1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of atomtypes for dihedral (4 instead of 2 or 4) (2) ERROR 2 [file ffoplsaabon.itp, line 2694]: Not enough parameters and then a lot of errors of the type: ERROR 3 [file S54.top, line 118]: No default Bond types ERROR 4 [file S54.top, line 120]: No default Bond types ERROR 5 [file S54.top, line 124]: No default Bond types ERROR 6 [file S54.top, line 127]: No default Bond types... Maybe the main question is for the third error is how to define these bond types and angles? Thank you. Elie > Date: Wed, 3 Oct 2012 22:09:02 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/3/12 7:48 PM, Elie M wrote: > > > > Sorry it seems that those breaks are due to hotmail and not present in the > > topology. Thanks for your reply. I still have problems...I will tell u > > briefly and as clear as possible what i did. > > (1) My top file has the following lines ate first: > > ; Include forcefield parameters #include "ffoplsaamod.itp"[ moleculetype ] > > which means that when grompp is reading it, it will first go to > > ffoplsaamod.itp. > > (2) After the description of what the ffoplsaamod is (commented by ";"), > > the input is simply: > > [ defaults ];nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 > > 3 yes 0.5 0.5 > > #include "ffoplsaanb.itp"#include "ffoplsaabon.itp" > > where the nonbonded and bonded parameters are included in this order (which > > you have also mentioned in your previous e-mail). If i run grompp in this > > way I get the error: > > Fatal error:Syntax error - File ffoplsaamod.itp, line 18Last line > > read:'\par'Found a second defaults directive. > > which I really cannot understand. The above [defaults] is the first thing > > that the code will pass through. How come it mentions this as a second > > directory? > > (3) i commented the above [ defaults] with a ";" and I get another error: > > Fatal error:Syntax error - File ffoplsaanb.itp, line 1Last line read:'[ > > atomtypes ]'Invalid order for directive atomtypes > > which might mean according to what I have read (correct me if I am wrong > > please), that the order might be violated and that [atomtypes] should not > > come first; but it is the first directive in the ffoplsaanb.itp file, which > > should be read first. > > So what might be happening? what is going wrong? or maybe what am I > > missing?Thank you all once again for the effort you are making in this forum > > > > It seems like the format of whatever files you're using is horribly broken. > I > would recommend starting over and not making any adjustments to any files > (removing lines, changing contents, adding comments, etc) unless you know > exactly what you're doing. For example, the presence of '\par' in > ffoplsaamod.itp suggests wrong line endings (i.e. from not using a plain text > editor). > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Error with "grompp"
Sorry it seems that those breaks are due to hotmail and not present in the topology. Thanks for your reply. I still have problems...I will tell u briefly and as clear as possible what i did. (1) My top file has the following lines ate first: ; Include forcefield parameters #include "ffoplsaamod.itp"[ moleculetype ] which means that when grompp is reading it, it will first go to ffoplsaamod.itp. (2) After the description of what the ffoplsaamod is (commented by ";"), the input is simply: [ defaults ];nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ1 3 yes 0.5 0.5 #include "ffoplsaanb.itp"#include "ffoplsaabon.itp" where the nonbonded and bonded parameters are included in this order (which you have also mentioned in your previous e-mail). If i run grompp in this way I get the error: Fatal error:Syntax error - File ffoplsaamod.itp, line 18Last line read:'\par'Found a second defaults directive. which I really cannot understand. The above [defaults] is the first thing that the code will pass through. How come it mentions this as a second directory? (3) i commented the above [ defaults] with a ";" and I get another error: Fatal error:Syntax error - File ffoplsaanb.itp, line 1Last line read:'[ atomtypes ]'Invalid order for directive atomtypes which might mean according to what I have read (correct me if I am wrong please), that the order might be violated and that [atomtypes] should not come first; but it is the first directive in the ffoplsaanb.itp file, which should be read first. So what might be happening? what is going wrong? or maybe what am I missing?Thank you all once again for the effort you are making in this forum Elie > Date: Wed, 3 Oct 2012 10:15:07 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/3/12 10:03 AM, Elie M wrote: > > > > Hello Emanuel. > > First of all thank you for your help. I am sorry if my previous e-mail was > > a bit confusing. I will tell what I did recently. > > (1) I removed all the information :molecule type, atoms, bonddihedral > > from my top file and pasted them to the ipt file , the one I called > > ffoplsaamod.itp; I also included an "#include command# referring to the > > .itp file. so my top file now just looks like that: > > " > > That doesn't really make any sense. You've chopped out the information for > your > molecule from the topology that g_x2top wrote, then simply re-included that > information? The output of g_x2top should be a functional topology; you > should > not have to adjust it. If you need this topology to be an .itp file, i.e. as > a > ligand in some other .top, then you only need to make small adjustments. See > the following: > > http://www.gromacs.org/Documentation/File_Formats/.itp_File > > > ;; File 'S54.top' was generated; By user: User (1000); On host: > > User-PC; At date: Wed Sep 26 01:43:14 2012;; This is your include > > topology file; Generated by x2top;#include "ffoplsaamod.itp" " > > and my foplsaamod.itp has the info that was present in .top file i.e: > > "[ moleculetype ] > > > > ; Namenrexcl > > > > S54NS 3 > > > > > > > > [ atoms ] > > > > ; nr > > type resnr residue atom > > cgnr charge mass > > typeBchargeB massB > > > > 1 > > opls_145 1LIG > > C 1 0 > > 12.011 ; qtot 0 > > > > 2 > > opls_735 1LIG > > C 2 0 > > 12.011 ; qtot 0 > > > > 3 > > opls_734 1LIG > > S 3 0 > > 32.06 ; qtot 0 > > > > 4 > > opls_735 1LIG > > C 4 0 > > 12.011 ; qtot 0 > > > > 5 > > opls_145 1 > > LIG C 5 > > 0 12.011 ; qtot 0 > > > > 6 > > opls_145 1LIG > > C 6 0 > > 12.011 ; qtot 0 > > > > 7 > > opls_516 1LIG > > C 7 0 > > 12.011 ; qtot 0 > > > > 8 > > opls_516 1LIG > > C 8 0 > > 12.011 ; qtot 0[ bonds ]...3736 > > 4283 1 > > > > 35 > > 373839 > > 1 > > > > 37 > > 383940 > > 1 > > > > 38 > > 394036 > > 1 > > > > 36 > > 404692 > >
RE: [gmx-users] Error with "grompp"
Hello Emanuel. First of all thank you for your help. I am sorry if my previous e-mail was a bit confusing. I will tell what I did recently. (1) I removed all the information :molecule type, atoms, bonddihedral from my top file and pasted them to the ipt file , the one I called ffoplsaamod.itp; I also included an "#include command# referring to the .itp file. so my top file now just looks like that: " ;; File 'S54.top' was generated; By user: User (1000); On host: User-PC; At date: Wed Sep 26 01:43:14 2012;; This is your include topology file; Generated by x2top;#include "ffoplsaamod.itp" " and my foplsaamod.itp has the info that was present in .top file i.e: "[ moleculetype ] ; Namenrexcl S54NS 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_145 1LIG C 1 0 12.011 ; qtot 0 2 opls_735 1LIG C 2 0 12.011 ; qtot 0 3 opls_734 1LIG S 3 0 32.06 ; qtot 0 4 opls_735 1LIG C 4 0 12.011 ; qtot 0 5 opls_145 1 LIG C 5 0 12.011 ; qtot 0 6 opls_145 1LIG C 6 0 12.011 ; qtot 0 7 opls_516 1LIG C 7 0 12.011 ; qtot 0 8 opls_516 1LIG C 8 0 12.011 ; qtot 0[ bonds ]...3736 4283 1 35 373839 1 37 383940 1 38 394036 1 36 404692 1 [ system ] ; Name S54NS [ molecules ] ; Compound#mols S54NS 1 "Have I missed something? i guess I did. I am getting an error of the form (when executing grompp_: Invalid order for directive [atoms]. (2) What about the ffoplsaabon.itp and ffoplsaanb.itp files? Do they have to be put somewhere. I am sorry to bombard u with all of this but I have got my head spinning thinking about topologies and fixing this error. Thank you Elie .> Date: Tue, 2 Oct 2012 03:56:28 + .> From: emanuel.bi...@monash.edu .> Subject: RE: [gmx-users] Error with "grompp" > To: gmx-users@gromacs.org > > Hi Elie, > > Your email is a bit confusing but I will try to give you some idea as per my > understanding of your email. > > If you want to use top and itp files separately, you should put all the info > (molecule type, atoms, bond, pairs, angles, dihedral) in your itp files and > you should use "# include "your itp file.itp" in your top file. No atom, > bond, pair etc in your top file. Just like you include your water type > (spc/tip4) you should include the itp. And top of that you should put the > right number of molecules in the right order in your top file at the > (molecules) section. > > Hope that might give you some help. > > Cheers, > Emanuel > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On > Behalf Of Elie M > Sent: Tuesday, 2 October 2012 1:39 PM > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] Error with "grompp" > > > I am a bit confused..I am getting different errors though similar in goal. > The error this time is: > "Fatal error:Syntax error - File S54.top, line 17Last line read:'[ atoms > ]'Invalid order for directive atoms"Let me tell you what I did again: I have > another n2t file ( fftoplsaamod.n2t) which was used to successfully produce > the .top file. Now since using grompp requires the presence of an > "ffoplsaamod.itp", i just copied the original ffoplsaa.itp and renamed it and > instead of it calling the two itp files :" ffoplsaanb.itp" and > ""ffoplsaabon.itp", I have included these two files (in the order they should > be) in the ffoplsaamod.itp file. What I am confised about is that the top > file has atoms, bonds, pairs,..whilst the .itp file has atomtypes, > bondtypeswhy is that? what should be done to circumvent the error? shall > all atomtypes in the itp be called atoms and bondtypes bonds to match that > .top file or what? and which file should be in the same order of which? > > Thanks > Elie > > > Date: Mon, 1 Oct 2012 08:38:15 -0400 > > From: jalem...@vt.edu > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] Error with "grompp" > > > > > > > > On 10/1/12 12:38 AM, Elie M wrote: > > > > > > Dear all, > > > Maybe this error has been discussed before; I have checked previous > > > messages on it but i
RE: [gmx-users] Error with "grompp"
I am a bit confused..I am getting different errors though similar in goal. The error this time is: "Fatal error:Syntax error - File S54.top, line 17Last line read:'[ atoms ]'Invalid order for directive atoms"Let me tell you what I did again: I have another n2t file ( fftoplsaamod.n2t) which was used to successfully produce the .top file. Now since using grompp requires the presence of an "ffoplsaamod.itp", i just copied the original ffoplsaa.itp and renamed it and instead of it calling the two itp files :" ffoplsaanb.itp" and ""ffoplsaabon.itp", I have included these two files (in the order they should be) in the ffoplsaamod.itp file. What I am confised about is that the top file has atoms, bonds, pairs,..whilst the .itp file has atomtypes, bondtypeswhy is that? what should be done to circumvent the error? shall all atomtypes in the itp be called atoms and bondtypes bonds to match that .top file or what? and which file should be in the same order of which? Thanks Elie > Date: Mon, 1 Oct 2012 08:38:15 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/1/12 12:38 AM, Elie M wrote: > > > > Dear all, > > Maybe this error has been discussed before; I have checked previous > > messages on it but i could not resolve it. I have done a modified version > > of the oplsaa forcefield which I have called "ffoplsaamod.n2t". The top > > file was created successfully. However when I run grompp, I get the error: > > "Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ > > bondtypes ]'" > > I tried to "uncomment" the bond types then the error moves to contraint > > types. What is the solution in this case? > > N.B: I have copied the file ffoplsaa.itp and called it "ffoplsaamod.itp".. > > Not sure if this has anything to do with the error. > > It probably does. The first #include statement in your topology is probably: > > #include "ffoplsaa.itp" > > That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp. If you have > renamed the files, then ffoplsaanb.itp does not occur and cannot be #included > prior to ffoplsaabon.itp. The order of inclusion is essential for proper > functionality. > > If you need to make adjustments to the contents of any of these files, make a > local copy of the entire force field and make modifications, leaving the > files > located in $GMXLIB alone. Do not rename them unless you consistently rename > all > references to these files. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Error with "grompp"
Thanks for your time and help as always. I will see what I can do about that. Elie > Date: Mon, 1 Oct 2012 08:38:15 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/1/12 12:38 AM, Elie M wrote: > > > > Dear all, > > Maybe this error has been discussed before; I have checked previous > > messages on it but i could not resolve it. I have done a modified version > > of the oplsaa forcefield which I have called "ffoplsaamod.n2t". The top > > file was created successfully. However when I run grompp, I get the error: > > "Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ > > bondtypes ]'" > > I tried to "uncomment" the bond types then the error moves to contraint > > types. What is the solution in this case? > > N.B: I have copied the file ffoplsaa.itp and called it "ffoplsaamod.itp".. > > Not sure if this has anything to do with the error. > > It probably does. The first #include statement in your topology is probably: > > #include "ffoplsaa.itp" > > That file, in turn, calls ffoplsaanb.itp and ffoplsaabon.itp. If you have > renamed the files, then ffoplsaanb.itp does not occur and cannot be #included > prior to ffoplsaabon.itp. The order of inclusion is essential for proper > functionality. > > If you need to make adjustments to the contents of any of these files, make a > local copy of the entire force field and make modifications, leaving the > files > located in $GMXLIB alone. Do not rename them unless you consistently rename > all > references to these files. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Error with "grompp"
Dear all, Maybe this error has been discussed before; I have checked previous messages on it but i could not resolve it. I have done a modified version of the oplsaa forcefield which I have called "ffoplsaamod.n2t". The top file was created successfully. However when I run grompp, I get the error: "Fatal error:Syntax error - File ffoplsaabon.itp, line 306Last line read:'[ bondtypes ]'" I tried to "uncomment" the bond types then the error moves to contraint types. What is the solution in this case? N.B: I have copied the file ffoplsaa.itp and called it "ffoplsaamod.itp".. Not sure if this has anything to do with the error. Thanks in advance, Elie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] .itp and .rtp file modifications?
Dear all, I am trying to minimize the energy of a polymer system I have. I have successfully modified the n2t file to include force fields for atoms that were not present. However now I am using "grompp" before using mdrun (to minimize). However I have a question should the .ITP and .RTP files be modified accordingly and if yes how is this possible? Any information of how to modify them? Elie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] a quick question (forgot to ask).
Sorry one more thing: For one of the atoms S that x2top did not assign the topology it said 0 bonds although S is a part of the Thiophene molecule which is connected to two carbons..what does it mean "0 bonds"? Thanks > From: elie.mouj...@hotmail.co.uk > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] error with x2top. > Date: Tue, 25 Sep 2012 22:17:21 +0100 > > > Yep You are right. I will try my best to change the files accordingly. > Thanks > > > Date: Tue, 25 Sep 2012 17:05:20 -0400 > > From: jalem...@vt.edu > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] error with x2top. > > > > > > > > On 9/25/12 5:02 PM, Elie M wrote: > > > > > > Thanks for your reply. I guess either way (x2top or pdb2gmx), I have > > > problems. pdb2gmx is giving the same old error residue 'UNK' is not > > > found in topology residue file whereas strangely enough x2top did not > > > complain and was able to assign topologies for 73 atoms out of 94 so > > > maybe it is easier to use x2top because in the other case I have to > > > change files and I have no experience in this whatsoever and I am really > > > tight on time. What do you personally think? > > > > > > > Neither tool is guaranteed to produce a topology for an arbitrary molecule. > > If > > g_x2top does not have the right parameters, it will fail. If pdb2gmx does > > not > > have the right parameters, it will fail. g_x2top further assumes that some > > generic set of atom types and functional groups will address whatever it is > > that > > you're working with. Sometimes that's appropriate, sometimes it's not. > > Either > > way, you're going to have to modify either the .n2t file or the .rtp file > > for > > your chosen force field. Regardless of the route you choose, you're going > > to > > have to come up with parameters for your molecule and learn how these files > > work > > so you can modify them. Parameterization is an expert topic for a reason. > > > > -Justin > > > > -- > > > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] error with x2top.
Yep You are right. I will try my best to change the files accordingly. Thanks > Date: Tue, 25 Sep 2012 17:05:20 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] error with x2top. > > > > On 9/25/12 5:02 PM, Elie M wrote: > > > > Thanks for your reply. I guess either way (x2top or pdb2gmx), I have > > problems. pdb2gmx is giving the same old error residue 'UNK' is not found > > in topology residue file whereas strangely enough x2top did not complain > > and was able to assign topologies for 73 atoms out of 94 so maybe it is > > easier to use x2top because in the other case I have to change files and I > > have no experience in this whatsoever and I am really tight on time. What > > do you personally think? > > > > Neither tool is guaranteed to produce a topology for an arbitrary molecule. > If > g_x2top does not have the right parameters, it will fail. If pdb2gmx does > not > have the right parameters, it will fail. g_x2top further assumes that some > generic set of atom types and functional groups will address whatever it is > that > you're working with. Sometimes that's appropriate, sometimes it's not. > Either > way, you're going to have to modify either the .n2t file or the .rtp file for > your chosen force field. Regardless of the route you choose, you're going to > have to come up with parameters for your molecule and learn how these files > work > so you can modify them. Parameterization is an expert topic for a reason. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] error with x2top.
Thanks for your reply. I guess either way (x2top or pdb2gmx), I have problems. pdb2gmx is giving the same old error residue 'UNK' is not found in topology residue file whereas strangely enough x2top did not complain and was able to assign topologies for 73 atoms out of 94 so maybe it is easier to use x2top because in the other case I have to change files and I have no experience in this whatsoever and I am really tight on time. What do you personally think? Regards > Date: Tue, 25 Sep 2012 16:32:33 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] error with x2top. > > > > On 9/25/12 4:28 PM, Elie M wrote: > > > > Dear all, > > i am trying to convert a .gro file into a top file using .x2top but not all > > atoms can be assigned forcefields and the code stops with the error: > > Generating bonds from distances...atom 94Can not find forcefield for atom > > C-2 with 2 bondsCan not find forcefield for atom S-3 with 0 bondsCan not > > find forcefield for atom C-4 with 2 bondsCan not find forcefield for atom > > C-7 with 3 bondsCan not find forcefield for atom C-10 with 3 bondsCan not > > find forcefield for atom S-12 with 0 bondsCan not find forcefield for atom > > C-13 with 2 bondsCan not find forcefield for atom C-16 with 2 bondsCan not > > find forcefield for atom O-17 with 2 bondsCan not find forcefield for atom > > O-18 withFatal error:Could only find a forcefield type for > > 73 out of 94 atoms > > I looked at the .atp and n2t files. I am not sure where to start. is the > > second column partial charges? how to determine these? are they > > automatically determined ..what about the numbers at the end after each > > atom symbol? Is there any clear examples of how to do this? Any help would > > be appreciated. Thanks > > > > The format is explained in full here: > > http://www.gromacs.org/Documentation/File_Formats/.n2t_File > > The charges and atom types are determined by parameterizing the molecule of > interest, but if you're going to do that much work, it's probably simpler to > create an .rtp entry and have pdb2gmx do the work. g_x2top is usually > intended > to create simple topologies for simple molecules. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] error with x2top.
Dear all, i am trying to convert a .gro file into a top file using .x2top but not all atoms can be assigned forcefields and the code stops with the error: Generating bonds from distances...atom 94Can not find forcefield for atom C-2 with 2 bondsCan not find forcefield for atom S-3 with 0 bondsCan not find forcefield for atom C-4 with 2 bondsCan not find forcefield for atom C-7 with 3 bondsCan not find forcefield for atom C-10 with 3 bondsCan not find forcefield for atom S-12 with 0 bondsCan not find forcefield for atom C-13 with 2 bondsCan not find forcefield for atom C-16 with 2 bondsCan not find forcefield for atom O-17 with 2 bondsCan not find forcefield for atom O-18 withFatal error:Could only find a forcefield type for 73 out of 94 atoms I looked at the .atp and n2t files. I am not sure where to start. is the second column partial charges? how to determine these? are they automatically determined ..what about the numbers at the end after each atom symbol? Is there any clear examples of how to do this? Any help would be appreciated. Thanks Elie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Missing charges in a .gro file
Thanks for your help. Elie > Date: Mon, 24 Sep 2012 13:05:14 +0800 > Subject: Re: [gmx-users] Missing charges in a .gro file > From: terrence...@gmail.com > To: gmx-users@gromacs.org > > On Mon, Sep 24, 2012 at 12:56 PM, Elie M wrote: > > > > > Dear all, > > I have created a .GRO file from a PDB file for a polymer. However in the > > PDB I have positive and negative charges of some ions where as in the > > produced GRO file these disappear. Are those charged atoms taken into > > account in the gro file as I will be doing a MD simulation of such polymers > > with nanotubes later and I dont want to work with the wrong GRO fileif > > the answer is no, how do I include them? Thanks > > Regards > > ELie -- > > > > http://manual.gromacs.org/online/gro.html > http://manual.gromacs.org/online/top.html > There are no charges in .gro files. The charges are probably discarded in > your way. > > Terry > > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Missing charges in a .gro file
Dear all, I have created a .GRO file from a PDB file for a polymer. However in the PDB I have positive and negative charges of some ions where as in the produced GRO file these disappear. Are those charged atoms taken into account in the gro file as I will be doing a MD simulation of such polymers with nanotubes later and I dont want to work with the wrong GRO fileif the answer is no, how do I include them? Thanks Regards ELie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Input/output error in GROMACS
Dear all, I am trying to use editconf to produce a .GRO file from an .XYZ file but I am getting the following error: "Program editconf, VERSION 4.0.5Source code file: futil.c, line: 330 File input/output error:S54NONSOLV.xyz.gro" Some of the input file is:46S54 NONSOLVATED POLYMERC 5.33751 -1.90290 0.0C 5.75001-2.61740 0.0S 5.19791-3.23050 0.0C 4.44431-2.89490 0.0C 4.53051-2.07440 0.0C 3.01530-2.89490 0.0C 3.72980-3.30740 0.0C 3.72980-4.13240 0.0C 3.01530 -4.54491 0.0C 2.30080-4.13240 0.0C 2.30080-3.30740 0.0... The XYZ format is right. Is it that editconf cannot read .XYZ files although I understood otherwise.. Thanks Elie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] use of PRODRG
Thanks for your time and help as usual. Elie > Date: Wed, 19 Sep 2012 13:47:26 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] use of PRODRG > > > > On 9/19/12 11:40 AM, Elie M wrote: > > > >> I don't understand this. PRODRG will be of no use here since you are using > >> OPLS-AA, and if there is no ligand, then why do you need some external > >> program > >> to build a topology? > > > > - The "LIG" residue only appears in the pdb version of the file. I tried > > to use editconf on the .mol type of file to change into .gro file but it > > gave an error so I thought editconf only changes pdb files into .gro ones. > > This raises a question: What other types of files does editconf change > > into .gro? Anyways, this is a part of the .mol file produced by Marvin > > Sketch: > > There is a list (somewhat cryptic if you're not used to reading it) in > src/gmxlib/filenm.c, which would suggest a variety of formats are acceptable, > but not .mol2 files. Most of the common ones (and some more exotic) can be > used: .pdb, .gro, .g96, .g87, .brk, .pqr, .xyz, .ent, .esp, and perhaps a few > more, just based on a quick scan. > > -Justin > > > Mrv0541 09081217542D > > 46 50 0 0 0 0999 V20005.3375 -1.90290. C > > 0 0 0 0 0 0 0 0 0 0 0 05.7500 -2.61740. C 0 0 > > 0 0 0 0 0 0 0 0 0 05.1979 -3.23050. S 0 0 0 0 > > 0 0 0 0 0 0 0 04.4443 -2.89490. C 0 0 0 0 0 0 > > 0 0 0 0 0 04.5305 -2.07440. C 0 0 0 0 0 0 0 0 > > 0 0 0 03.0153 -2.89490. C 0 0 0 0 0 0 0 0 0 0 > > 0 03.7298 -3.30740. C 0 0 0 0 0 0 0 0 0 0 0 0 > > 3.7298 -4.13240. C 0 0 0 0 0 0 0 0 0 0 0 0 > > 3.0153 -4.54490. C 0 0 0 0 0 0 0 0 0 0 0 02.3008 > > -4.13240. C 0 0 0 0 0 0 0 0 0 0 0 02.3008 > > -3.30740. C 0 0 0 0 0 0 0 0 0 0 0 00.8327 > > -4.20930. S 0 0 0 0 0 0 0 0 0 0 0 0.. > > Thanks for your help > > Elie > > > > > >> Date: Wed, 19 Sep 2012 05:23:28 -0400 > >> From: jalem...@vt.edu > >> To: gmx-users@gromacs.org > >> Subject: Re: [gmx-users] use of PRODRG > >> > >> > >> > >> On 9/18/12 10:35 PM, Elie M wrote: > >>> > >>> Dear all, > >>> I have been reading about PRODRG that takes a PDB file as an input and > >>> produces topologies compatible with GROMACS as an output. Can this > >>> program be then considered as a solution to the problem of missing > >>> residues in GROMACS like LIG? > >> > >> PRODRG produces topologies for the Gromos96 43a1 parameter set (and an > >> older > >> version produces topologies for the outdated Gromos87), and the quality of > >> the > >> topologies is generally very low. The resulting topologies require > >> significant > >> modification. > >> > >>> N.B: I am using the OPLSAA force field .I also have the files in MDL > >>> MOL2 version which do not contain the LIG residue appearing in the PDB > >>> file. So maybe using PRODRG on the MOL2 might solve the problem? > >> > >> I don't understand this. PRODRG will be of no use here since you are using > >> OPLS-AA, and if there is no ligand, then why do you need some external > >> program > >> to build a topology? > >> > >> -Justin > >> > >> -- > >> > >> > >> Justin A. Lemkul, Ph.D. > >> Research Scientist > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) 231-9080 > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >> > >> -- > >> gmx-users mailing listgmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >
RE: [gmx-users] use of PRODRG
> I don't understand this. PRODRG will be of no use here since you are using > OPLS-AA, and if there is no ligand, then why do you need some external > program > to build a topology? - The "LIG" residue only appears in the pdb version of the file. I tried to use editconf on the .mol type of file to change into .gro file but it gave an error so I thought editconf only changes pdb files into .gro ones. This raises a question: What other types of files does editconf change into .gro? Anyways, this is a part of the .mol file produced by Marvin Sketch: Mrv0541 09081217542D 46 50 0 0 0 0999 V20005.3375 -1.90290. C 0 0 0 0 0 0 0 0 0 0 0 05.7500 -2.61740. C 0 0 0 0 0 0 0 0 0 0 0 05.1979 -3.23050. S 0 0 0 0 0 0 0 0 0 0 0 04.4443 -2.89490. C 0 0 0 0 0 0 0 0 0 0 0 0 4.5305 -2.07440. C 0 0 0 0 0 0 0 0 0 0 0 03.0153 -2.89490. C 0 0 0 0 0 0 0 0 0 0 0 03.7298 -3.3074 0. C 0 0 0 0 0 0 0 0 0 0 0 03.7298 -4.13240. C 0 0 0 0 0 0 0 0 0 0 0 03.0153 -4.54490. C 0 0 0 0 0 0 0 0 0 0 0 02.3008 -4.13240. C 0 0 0 0 0 0 0 0 0 0 0 02.3008 -3.30740. C 0 0 0 0 0 0 0 0 0 0 0 00.8327 -4.20930. S 0 0 0 0 0 0 0 0 0 0 0 0.. Thanks for your help Elie > Date: Wed, 19 Sep 2012 05:23:28 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] use of PRODRG > > > > On 9/18/12 10:35 PM, Elie M wrote: > > > > Dear all, > > I have been reading about PRODRG that takes a PDB file as an input and > > produces topologies compatible with GROMACS as an output. Can this program > > be then considered as a solution to the problem of missing residues in > > GROMACS like LIG? > > PRODRG produces topologies for the Gromos96 43a1 parameter set (and an older > version produces topologies for the outdated Gromos87), and the quality of > the > topologies is generally very low. The resulting topologies require > significant > modification. > > > N.B: I am using the OPLSAA force field .I also have the files in MDL MOL2 > > version which do not contain the LIG residue appearing in the PDB file. So > > maybe using PRODRG on the MOL2 might solve the problem? > > I don't understand this. PRODRG will be of no use here since you are using > OPLS-AA, and if there is no ligand, then why do you need some external > program > to build a topology? > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] use of PRODRG
Dear all, I have been reading about PRODRG that takes a PDB file as an input and produces topologies compatible with GROMACS as an output. Can this program be then considered as a solution to the problem of missing residues in GROMACS like LIG? N.B: I am using the OPLSAA force field .I also have the files in MDL MOL2 version which do not contain the LIG residue appearing in the PDB file. So maybe using PRODRG on the MOL2 might solve the problem? Regards Elie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] energy minimisation of carbon nanotubes.
Thank you for your reply and help. Regards Elie > Date: Sat, 15 Sep 2012 13:32:06 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] energy minimisation of carbon nanotubes. > > > > On 9/15/12 12:49 PM, Elie M wrote: > > > > Dear all, > > I have a small question regarding energy minimization. I am minimizing a > > carbon naotube in vaccuo and my (mdp )input file is: ; > > > > ; SWNT (10,0) on its own > > > > ; Elie Moujaes, SWNT+polymers project > > > > ; Energy minimization input file > > > > ; > > > > cpp =/usr/bin/cpp > > > > define = > > -DFLEXIBLE > > > > constraints = > > none > > > > integrator = > > cg > > > > nsteps = > > 2000 > > > > ; > > > > ; Energy minimizing stuff > > > > ; > > > > emtol = 0.1 > > > > emstep = > > 0.03 > > > > > > > > nstcomm = > > 1 > > > > pbc = xyz > > > > periodic_molecules = yes > > > > ns_type = > > grid > > > > rlist = 1 > > > > rcoulomb= 1.0 > > > > rvdw= 1.0 > > > > Tcoupl = > > no > > > > Pcoupl = > > no > > > > gen_vel = > > no > > I have put emstep very loww toa chieve accuracy.In the output i got: > > Reading file SWNT-EM.tpr, VERSION 4.0.5 (single precision)Polak-Ribiere > > Conjugate Gradients: Tolerance (Fmax) = 1.0e-05 Number of steps > > = 2000 F-max = 3.48055e+03 on atom 799 F-Norm > > = 9.67779e+02 > > > > Stepsize too small, or no change in energy.Converged to machine > > precision,but not to the requested precision Fmax < 1e-05 > > Double precision normally gives you higher accuracy. > > writing lowest energy coordinates. > > Polak-Ribiere Conjugate Gradients converged to machine precision in 359 > > steps,but did not reach the requested Fmax < 1e-05.Potential Energy = > > 8.7646348e+03Maximum force = 1.6186214e+01 on atom 701Norm of force > > = 5.4860659e+00 > > It seems that I have to use the double precision version but as the single > > precision is concerned,Is the minimization fine (as the maximum force on > > atom 701 is 16...)? > > The outcome seems reasonable. I doubt that any algorithm, in single or > double > precision, would ever reach Fmax < 1e-05. Values of Fmax < 10 are generally > suitable for just about any purpose and Fmax < 1000 will generally result in > stable simulations for most systems. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] energy minimisation of carbon nanotubes.
Dear all, I have a small question regarding energy minimization. I am minimizing a carbon naotube in vaccuo and my (mdp )input file is: ; ; SWNT (10,0) on its own ; Elie Moujaes, SWNT+polymers project ; Energy minimization input file ; cpp =/usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = cg nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 0.1 emstep = 0.03 nstcomm = 1 pbc = xyz periodic_molecules = yes ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I have put emstep very loww toa chieve accuracy.In the output i got: Reading file SWNT-EM.tpr, VERSION 4.0.5 (single precision)Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.0e-05 Number of steps= 2000 F-max = 3.48055e+03 on atom 799 F-Norm = 9.67779e+02 Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax < 1e-05 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to machine precision in 359 steps,but did not reach the requested Fmax < 1e-05.Potential Energy = 8.7646348e+03Maximum force = 1.6186214e+01 on atom 701Norm of force = 5.4860659e+00 It seems that I have to use the double precision version but as the single precision is concerned,Is the minimization fine (as the maximum force on atom 701 is 16...)? Thanks Elie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Segmentation fault (core dumped error)
Thanks very much for much for your help. The Carbon naotube issue is solved. I still have to figure out the polymers. Thanks for the info Regards Elie > Date: Fri, 14 Sep 2012 10:31:28 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Segmentation fault (core dumped error) > > > > On 9/14/12 12:19 AM, Elie M wrote: > > > > Dear all, I am trying to study the MD of a Carbon Nanotube interacting with > > some polymers. and I have some problems in forming the topology files. I > > have actually two questions and I hope you can help me in that. > > (1) In an attempt to form the topology files of CNTs and graphene (using > > x2top), i have found on the internet scripts (by Andrea Minoia I guess). > > These constitute of adding .nt2, .rtp. and .itp files to the > > /Gromacs/share/Gromacs/top directory (namely ffcntoplsaa.nt2, > > ffcntoplsaa.rtp and ffcntoplsaa.itp) and adding a line in the FF.dat file. > > I have done that and tried to execute x2top and I got the error: > > "..Entries in elements.dat: 218Looking whether force field files > > existOpening library file > > /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.rtpOpening > > library file > > /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tOpening > > library file > > /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tThere are 0 > > name to type translationsGenerating bonds from distances...Segmentation > > fault (core dumped)" > > Can anyone please tell me the source of this error and how to fix it? > > x2top is telling you it found nothing in the .n2t file. Either the contents > are > nonexistent, formatted incorrectly, or you have a line ending issue (common > with > Windows OS - use dos2unix if necessary). > > > (2) I will definitely need a top file for the polymers I will also be > > solvating. But I also have problems because the pdb file contains a LIG > > residue unrecognizable by Gromacs. I have asked this question before and I > > was advised to change some files accordingly but to be honest I am not > > really professional in that; I have asked someone who had a problem in the > > past but he did not know all the details because he ended up not using the > > modified force fields after all. Can anyone give me in details how to > > incorporate the residue "LIG" within the force field or let me know whom I > > can consult...A part of the pdb file with the residue LIG is: > > "COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.1HETATM1 C > > LIG 1 1.481 -1.276 -0.621 1.00 0.00 CHETATM2 C > > LIG 1 2.216 -2.370 -1.040 1.00 0.00 CHETATM3 > > S LIG 1 3.770 -2.409 -0.306 1.00 0.00 SHETATM > > 4 C LIG 1 3.456 -0.998 0.609 1.00 0.00 CHETATM > > 5 C LIG 1 2.207 -0.479 0.313 1.00 0.00 > > CHETATM6 C LIG 1 5.156 0.676 1.386 1.00 0.00 > > CHETATM7 C LIG 1 4.423 -0.491 1.600 1.00 0.00 > > CHETATM8 C LIG 1 4.550 -1.119 2.847 1.00 0.00 > > CHETATM9 C LIG 1 5.256 -0.503 3.905 1.00 0.00 > > CHETATM 10 C LIG 1 6.107 0.592 3.667 1.00 0.00 > > CHETATM 11 C LIG 1 6.008 1.181 2.393 1.00 > > 0.00 CHETATM 12 S LIG 1 7.457 2.548 5.198 > > 1.00 0.00 ! > SHETA > TM 13 C LIG 1 7.220 0.945 4.621 1.00 0.00..." > > You need to introduce some sensible set of parameters for it. Using a > generic > "LIG" for a polymer is unlikely to work. Consult the following: > > http://www.gromacs.org/Documentation/How-tos/Polymers > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or sen
[gmx-users] Segmentation fault (core dumped error)
Dear all, I am trying to study the MD of a Carbon Nanotube interacting with some polymers. and I have some problems in forming the topology files. I have actually two questions and I hope you can help me in that. (1) In an attempt to form the topology files of CNTs and graphene (using x2top), i have found on the internet scripts (by Andrea Minoia I guess). These constitute of adding .nt2, .rtp. and .itp files to the /Gromacs/share/Gromacs/top directory (namely ffcntoplsaa.nt2, ffcntoplsaa.rtp and ffcntoplsaa.itp) and adding a line in the FF.dat file. I have done that and tried to execute x2top and I got the error: "..Entries in elements.dat: 218Looking whether force field files existOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.rtpOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tThere are 0 name to type translationsGenerating bonds from distances...Segmentation fault (core dumped)" Can anyone please tell me the source of this error and how to fix it? (2) I will definitely need a top file for the polymers I will also be solvating. But I also have problems because the pdb file contains a LIG residue unrecognizable by Gromacs. I have asked this question before and I was advised to change some files accordingly but to be honest I am not really professional in that; I have asked someone who had a problem in the past but he did not know all the details because he ended up not using the modified force fields after all. Can anyone give me in details how to incorporate the residue "LIG" within the force field or let me know whom I can consult...A part of the pdb file with the residue LIG is: "COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.1HETATM1 C LIG 1 1.481 -1.276 -0.621 1.00 0.00 CHETATM2 C LIG 1 2.216 -2.370 -1.040 1.00 0.00 CHETATM3 S LIG 1 3.770 -2.409 -0.306 1.00 0.00 SHETATM4 C LIG 1 3.456 -0.998 0.609 1.00 0.00 CHETATM5 C LIG 1 2.207 -0.479 0.313 1.00 0.00 CHETATM6 C LIG 1 5.156 0.676 1.386 1.00 0.00 CHETATM7 C LIG 1 4.423 -0.491 1.600 1.00 0.00 CHETATM8 C LIG 1 4.550 -1.119 2.847 1.00 0.00 CHETATM9 C LIG 1 5.256 -0.503 3.905 1.00 0.00 CHETATM 10 C LIG 1 6.107 0.592 3.667 1.00 0.00 CHETATM 11 C LIG 1 6.008 1.181 2.393 1.00 0.00 CHETATM 12 S LIG 1 7.457 2.548 5.198 1.00 0.00 SHETATM 13 C LIG 1 7.220 0.945 4.621 1.00 0.00..." I am really thankful Elie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] error in producing top file for a structure
Thanks very much for the help. I will see what I can do about that. Sincerely ELie > Date: Sat, 8 Sep 2012 16:50:00 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] error in producing top file for a structure > > > > On 9/8/12 4:46 PM, Elie M wrote: > > > > > > Thanks a lot for your response. Actually i do have LIG , which obviosuly the > > code did not understand and changed it into LI; at first I thought LI was > > LIG > > but in GROMACS' language. Is there any place where I can read how to > > implement changes in the .rtp file? or any other way to get the correct pdb > > format. i used openbabel because Markin SKETCH and ArgusLAB do not seem to > > keep the charged Nitrogen and Chlorine ions I have got in my structure. By > > the way, I have attached the pdb input file (I guess).. > > > > The list does not accept attachments. If Gromacs is interpreting "LIG" as > "LI" > then the .pdb file is formatted incorrectly - at least one column is shifted, > which will lead to misinterpretation of all of the contents. If you want to > add > a new residue in the .rtp file, refer to the manual, section 5.6.1, in > conjunction with implementation details at: > > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] error in producing top file for a structure
Thanks a lot for your response. Actually i do have LIG , which obviosuly the code did not understand and changed it into LI; at first I thought LI was LIG but in GROMACS' language. Is there any place where I can read how to implement changes in the .rtp file? or any other way to get the correct pdb format. i used openbabel because Markin SKETCH and ArgusLAB do not seem to keep the charged Nitrogen and Chlorine ions I have got in my structure. By the way, I have attached the pdb input file (I guess).. Thanks once again Elie > Date: Sat, 8 Sep 2012 16:37:16 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] error in producing top file for a structure > > > > On 9/8/12 4:29 PM, Elie M wrote: > > > > Dear all, > > I am new to GROMACS. I am trying to minimize a structure but first I have > > to form the pdb file with the correct force field parameters. I am using > > version 4.0.5 and an OPLSAA force field. The error I am getting > > is:...Opening library file > > /cygdrive/c/Packages/Gromacs/share/gromacs/top/ffOPLSAA-c.tdbProcessing > > chain 1 (46 atoms, 1 residues)There are 4 donors and 2 acceptorsThere are 0 > > hydrogen bonds > > ---Program pdb2gmx, > > VERSION 4.0.5Source code file: pdb2gmx.c, line: 429 > > Fatal error:Atom C in residue LI 1 not found in rtp entry with 1 atoms > >while sorting > > atoms--- > > I read about the error but i could not figure out the "mismatch" that was > > stated in the input file which you will find attached. Please can anyone > > help me > > The error comes from the fact that pdb2gmx is finding a carbon atom in a > residue > named LI (which is lithium). Of course, that is nonsense. Without seeing > the > .pdb file, it's hard to say what's going on, but if you have some residue > named > "LIG" (which will also be unknown to pdb2gmx) then perhaps the format of the > .pdb file is wrong. That's just a wild guess though. But of course, if you > have "LIG" then you will need to add all the necessary parameters to the .rtp > file anyway. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] error in producing top file for a structure
Dear all, I am new to GROMACS. I am trying to minimize a structure but first I have to form the pdb file with the correct force field parameters. I am using version 4.0.5 and an OPLSAA force field. The error I am getting is:...Opening library file /cygdrive/c/Packages/Gromacs/share/gromacs/top/ffOPLSAA-c.tdbProcessing chain 1 (46 atoms, 1 residues)There are 4 donors and 2 acceptorsThere are 0 hydrogen bonds ---Program pdb2gmx, VERSION 4.0.5Source code file: pdb2gmx.c, line: 429 Fatal error:Atom C in residue LI 1 not found in rtp entry with 1 atoms while sorting atoms--- I read about the error but i could not figure out the "mismatch" that was stated in the input file which you will find attached. Please can anyone help me ThankssN.B: The pdb format of the inout file is produced using OPENBABEL. Elie MUniversity of NottsNG7 2RDUK -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
