[gmx-users] gromacs.org_gmx-users Digest, Vol 180, Issue 46
Ayesha Fatima
ayeshafatima.69 at gmail.com
Sun Apr 14 12:08:43 CEST 2019
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-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
> >
> > * 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: 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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