Thank you Rahul for the response. I tried that but still cant see it. In addition to my previous question,. how do we restrain the lipid membrane in one direction only. I came across the GROMACS documentation where it sytes the freedim parameter. Is it placed in the pull md parameter file of elsewhere? Thank you
On Sun, Apr 14, 2019 at 1:53 PM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: Problem regarding grompp command (Encountered a second > block of parameters for dihedral type 9 for the same atoms...) > (RAHUL SURESH) > 2. Re: Problem regarding grompp command (Encountered a second > block of parameters for dihedral type 9 for the same atoms...) > (RAHUL SURESH) > 3. make index for protein multiple ligand md simulation (m mar) > 4. Re: make index for protein multiple ligand md simulation > (Soham Sarkar) > 5. GMO simulation (Ayesha Fatima) > 6. Re: GMO simulation (RAHUL SURESH) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 14 Apr 2019 00:50:10 +0530 > From: RAHUL SURESH <drrahulsur...@gmail.com> > To: gmx-us...@gromacs.org > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Problem regarding grompp command (Encountered > a second block of parameters for dihedral type 9 for the same > atoms...) > Message-ID: > < > caatfitssehgq-cuqkfejas0p9f1rwxfbpkwabftbhzrrads...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi > > You have messed different versions of prm and charmm file. Please have a > check with the charmm generated prm and FF files. > > Thank you > > > On Thu 4 Apr, 2019, 7:05 PM Chem, <chemanaly...@yahoo.com> wrote: > > > To > > Prof. Justin A. Lemkul &Gromacs Users > > Dear Gromacs users > > > > I am learning MD simulation of protein-ligand interaction using an > > important Gromacs software, applied to my compound; 3b-Acetoxy-6-nitro > > cholest-5-ene.When I implemented the commands given below. I faced the > > problem.I read many questions and answers related to my problem, but I > > could not find the appropriate answer. > > > > $ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr > > ERROR 11 [file unk.prm, line 264]: > > > > Encountered a second block of parameters for dihedral type 9 for the > same > > > > atoms, with either different parameters and/or the first block has > > > > multiple lines. This is not supported. > > > > > > > > ERROR 12 [file unk.prm, line 265]: > > > > Encountered a second block of parameters for dihedral type 9 for the > same > > > > atoms, with either different parameters and/or the first block has > > > > multiple lines. This is not supported. > > > > > > > > Line 264 CG3C52 CG3C52 CG3RC1 CG311 9 > > 0.000000 0.418400 3 > > > > Line 265 CG3C52 CG3C52 CG3RC1 CG311 9 > > 0.000000 2.092000 4 > > > > . > > > > . > > > > > > > > > > > > > ................................................................................................................... > > > > I need your kind help to overcome this problem, so I learn the simulation > > smoothly > > > > I look forward to your useful help with the above problem > > > > Please suggest me what I should do > > > > > > > > > > Regards > > M. Alam > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > ------------------------------ > > Message: 2 > Date: Sun, 14 Apr 2019 00:50:10 +0530 > From: RAHUL SURESH <drrahulsur...@gmail.com> > To: gmx-us...@gromacs.org > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Problem regarding grompp command (Encountered > a second block of parameters for dihedral type 9 for the same > atoms...) > Message-ID: > < > caatfitssehgq-cuqkfejas0p9f1rwxfbpkwabftbhzrrads...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi > > You have messed different versions of prm and charmm file. Please have a > check with the charmm generated prm and FF files. > > Thank you > > > On Thu 4 Apr, 2019, 7:05 PM Chem, <chemanaly...@yahoo.com> wrote: > > > To > > Prof. Justin A. Lemkul &Gromacs Users > > Dear Gromacs users > > > > I am learning MD simulation of protein-ligand interaction using an > > important Gromacs software, applied to my compound; 3b-Acetoxy-6-nitro > > cholest-5-ene.When I implemented the commands given below. I faced the > > problem.I read many questions and answers related to my problem, but I > > could not find the appropriate answer. > > > > $ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr > > ERROR 11 [file unk.prm, line 264]: > > > > Encountered a second block of parameters for dihedral type 9 for the > same > > > > atoms, with either different parameters and/or the first block has > > > > multiple lines. This is not supported. > > > > > > > > ERROR 12 [file unk.prm, line 265]: > > > > Encountered a second block of parameters for dihedral type 9 for the > same > > > > atoms, with either different parameters and/or the first block has > > > > multiple lines. This is not supported. > > > > > > > > Line 264 CG3C52 CG3C52 CG3RC1 CG311 9 > > 0.000000 0.418400 3 > > > > Line 265 CG3C52 CG3C52 CG3RC1 CG311 9 > > 0.000000 2.092000 4 > > > > . > > > > . > > > > > > > > > > > > > ................................................................................................................... > > > > I need your kind help to overcome this problem, so I learn the simulation > > smoothly > > > > I look forward to your useful help with the above problem > > > > Please suggest me what I should do > > > > > > > > > > Regards > > M. Alam > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > ------------------------------ > > Message: 3 > Date: Sun, 14 Apr 2019 03:14:09 +0430 > From: m mar <sm.marashi...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] make index for protein multiple ligand md > simulation > Message-ID: > <CAFiRKKWZiX8Fg7C4xB9NUyHgd6PhMQk-5t= > cz8rchmmx_pd...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > dear users > I want to run md simulation for protein with cofactor and ligand > simultaneously, but I dont know how I should merge protein and ligands > together in make index step . > thanks for your help > > > ------------------------------ > > Message: 4 > Date: Sun, 14 Apr 2019 08:45:49 +0530 > From: Soham Sarkar <soham9...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] make index for protein multiple ligand md > simulation > Message-ID: > <CA+fBedfLrWH1bv9c03pEoUc0ZyYogJ7UP+1k= > 5v0rvcypg4...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > It should be > > Protein_index_number | ligand_index_number | cofactor_index_number > (In a single line) > > and you are done!!! > > On Sun, 14 Apr 2019, 4:14 am m mar, <sm.marashi...@gmail.com> wrote: > > > dear users > > I want to run md simulation for protein with cofactor and ligand > > simultaneously, but I dont know how I should merge protein and ligands > > together in make index step . > > thanks for your help > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > ------------------------------ > > Message: 5 > Date: Sun, 14 Apr 2019 13:44:49 +0800 > From: Ayesha Fatima <ayeshafatima...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] GMO simulation > Message-ID: > <CAHpQfU2JqCS54XYEh=8L0iveQtnG= > cn3g4mek4lznhdz8sf...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear All, > I have a glyceryl monooleate 100 molecule assembly. I want to pull a > peptide like molecule through it. I have obtained the forcefield files > from *Boeckmann, > Rainer website.* > I followed the Bevan Lab KAlp15 tutorial to build topology of lipids but > got stuck as the force field obtained from Rainer website and put in the > working directory, the path to working directory does not appear in the > list of forcefields. > i prepared my molecule using 54a7 forcefield implemented in ATB server. i > got the itp files and prepared the gro file using editconf > My question is to anyone who has done the glycerol simulation using > gromacs. please help with the exact procedure to develop the simulation > files. Should I add the 54a7 forcefield with to the OPLSAA updated > forcefield by Prof Rainer or vice versa? I also have a peptide like > molecule to pull through the GMO membrane. Any one can help guide through > this? > > Thank you in anticipation > Ayesha > > > ------------------------------ > > Message: 6 > Date: Sun, 14 Apr 2019 11:21:44 +0530 > From: RAHUL SURESH <drrahulsur...@gmail.com> > To: gmx-us...@gromacs.org > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] GMO simulation > Message-ID: > < > caatfitvwfk52gyqsu307vj+dm2otjdehxtgjaavdw+mmdms...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > On Sun 14 Apr, 2019, 11:15 AM Ayesha Fatima, <ayeshafatima...@gmail.com> > wrote: > > > Dear All, > > I have a glyceryl monooleate 100 molecule assembly. I want to pull a > > peptide like molecule through it. I have obtained the forcefield files > > from *Boeckmann, > > Rainer website.* > > I followed the Bevan Lab KAlp15 tutorial to build topology of lipids but > > got stuck as the force field obtained from Rainer website and put in the > > working directory, the path to working directory does not appear in the > > list of forcefields. > > i prepared my molecule using 54a7 forcefield implemented in ATB server. i > > got the itp files and prepared the gro file using editconf > > My question is to anyone who has done the glycerol simulation using > > gromacs. please help with the exact procedure to develop the simulation > > files. Should I add the 54a7 forcefield with to the OPLSAA updated > > forcefield by Prof Rainer or vice versa? I also have a peptide like > > molecule to pull through the GMO membrane. Any one can help guide through > > this? > > > > Hi > > You must add the ff in Ur gromacs directory and not in Ur working > directory. > > For example, use/local/gromacs/share/gromacs/top > > And that will reflect the FF in pdb2gmx. > > > > > Thank you in anticipation > > Ayesha > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 180, Issue 46 > ****************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.