[gmx-users] gromacs.org_gmx-users Digest, Vol 180, Issue 46
RAHUL SURESH
drrahulsuresh at gmail.com
Sun Apr 14 12:16:53 CEST 2019
On Sun 14 Apr, 2019, 3:39 PM Ayesha Fatima, <ayeshafatima.69 at gmail.com>
wrote:
> 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
Do you mean, you want to have membrane as pulling reference parameter?
>
>
>
>
> On Sun, Apr 14, 2019 at 1:53 PM <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
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> > 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 <drrahulsuresh at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc: gromacs.org_gmx-users at 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-CUqKfEJaS0p9f1RwXfbPkWaBfTbHzrRADs0KQ at 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, <chemanalyser at 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
> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sun, 14 Apr 2019 00:50:10 +0530
> > From: RAHUL SURESH <drrahulsuresh at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc: gromacs.org_gmx-users at 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-CUqKfEJaS0p9f1RwXfbPkWaBfTbHzrRADs0KQ at 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, <chemanalyser at 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-request at gromacs.org.
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Sun, 14 Apr 2019 03:14:09 +0430
> > From: m mar <sm.marashiyan at gmail.com>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] make index for protein multiple ligand md
> > simulation
> > Message-ID:
> > <CAFiRKKWZiX8Fg7C4xB9NUyHgd6PhMQk-5t=
> > cZ8rChMMX_PDzbg at 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 <soham9038 at gmail.com>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] make index for protein multiple ligand md
> > simulation
> > Message-ID:
> > <CA+fBedfLrWH1bv9c03pEoUc0ZyYogJ7UP+1k=
> > 5V0rvcypG4LwQ at 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.marashiyan at 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-request at gromacs.org.
> > >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Sun, 14 Apr 2019 13:44:49 +0800
> > From: Ayesha Fatima <ayeshafatima.69 at gmail.com>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: [gmx-users] GMO simulation
> > Message-ID:
> > <CAHpQfU2JqCS54XYEh=8L0iveQtnG=
> > cN3G4mEK4LZNHdz8sfWyQ at 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 <drrahulsuresh at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: Re: [gmx-users] GMO simulation
> > Message-ID:
> > <
> > CAAtfiTvWFk52gYqsU307Vj+DM2otJDeHxTgjaavDW+MmDms9+Q at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > On Sun 14 Apr, 2019, 11:15 AM Ayesha Fatima, <ayeshafatima.69 at 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-request at 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-request at gromacs.org.
> >
> > End of gromacs.org_gmx-users Digest, Vol 180, Issue 46
> > ******************************************************
> >
> --
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