[gmx-users] Regarding gromacs commands..

Mon Jan 9 19:25:09 CET 2017

Hi,

I mean in this thread

Mark

On Mon, Jan 9, 2017 at 7:16 PM Thomas Allen <thomas.c.allen at rice.edu> wrote:

> Which thread do you mean? I'd be happy to take a look, but I'm new to
> the mailing list and having some trouble finding the right search
> keywords for the archive.
>
> -Tom
>
> Quoting Mark Abraham <mark.j.abraham at gmail.com>:
>
> > Hi,
> >
> > Justin suggested a useful procedure a few emails back. Have you tried it?
> >
> > Mark
> >
> > On Mon, 9 Jan 2017 17:36 Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
> >
> >> Sir, i want to run an simulation of 300 molecules of ammonia...
> >> how can i proceed with it..??
> >> can u please help me out....
> >>
> >>
> >>
> >>  Sent with Mailtrack
> >> <
> >>
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >> >
> >>
> >> On Mon, Jan 9, 2017 at 9:37 AM, Dilip H N <cy16f01.dilip at nitk.edu.in>
> >> wrote:
> >>
> >> > 1] I want to simulate ammonia.....
> >> > 2] if i am creating in the avogadro molecular editor for 216
> molecules of
> >> > ammonia.. it is not writing the residue no. ie., for 1 NH3, it should
> >> write
> >> > 1111(4atoms),next NH3 2222..., and in this file below, the z axis is
> >> almost
> >> > same...ie., 50.037,49.75....how can i alter the z axis
> >> > 3]i tired to generate the topology from the perl interprter....
> >> > 4] gmx grompp -f file.mdp -c file.gro -p file.top
> >> > 5] gmx mdrun -v deffnm em -s file.tpr
> >> > and it gace me segmentation error....
> >> > here is the .mdp file, .pdb file
> >> >
> >> >
> >> >
> >> >  Sent with Mailtrack
> >> > <
> >>
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >> >
> >> >
> >> > On Sun, Jan 8, 2017 at 10:22 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> >> >
> >> >>
> >> >>
> >> >> On 1/7/17 10:58 PM, Dilip H N wrote:
> >> >>
> >> >>> can i create it with Avogadro molecular editor software..??
> >> >>>
> >> >>
> >> >> Probably, but that's a question for whatever help forum they provide.
> >> >>
> >> >> I tried creating using this software,, than if i compile it and run
> the
> >> >>> command of mdrun......
> >> >>> it is giving segmentation fault....
> >> >>> how to rectify it..??
> >> >>>
> >> >>>
> >> >> Not a clue.  There are a ton of steps between "create a PDB file" and
> >> >> "execute mdrun," none of which you've shown us.  If you want detailed
> >> help,
> >> >> you have to provide detailed information (steps taken, exact commands
> >> >> given, text of input files and what you're trying to accomplish,
> etc).
> >> We
> >> >> can't read your mind.  A seg fault is a catastrophic failure of the
> >> >> physical model due to problems with any number of things.  It's not
> >> >> productive for anyone to guess.
> >> >>
> >> >>
> >> >> -Justin
> >> >>
> >> >>
> >> >>>
> >> >>>  Sent with Mailtrack
> >> >>> <https://mailtrack.io/install?source=signature&lang=en&refer
> >> >>> ral=cy16f01.dilip at nitk.edu.in&idSignature=22>
> >> >>>
> >> >>> On Sat, Jan 7, 2017 at 12:15 AM, Justin Lemkul <jalemkul at vt.edu>
> >> wrote:
> >> >>>
> >> >>>
> >> >>>>
> >> >>>> On 1/6/17 2:24 AM, Dilip H N wrote:
> >> >>>>
> >> >>>> no...
> >> >>>>> I want to create  300 molecules of ammonia...
> >> >>>>>
> >> >>>>>
> >> >>>> Well, you asked about BF3, so you got an answer about BF3 :)
> >> >>>>
> >> >>>> how can i create  300 molecules of ammonia and then get it in .pdb
> >> file
> >> >>>>
> >> >>>>> format..??
> >> >>>>>
> >> >>>>>
> >> >>>>> For a simple molecule like NH3 you can easily write the
> coordinates
> >> by
> >> >>>> hand from basic geometry.  Otherwise, find an NMR structure of a
> >> protein
> >> >>>> that contains Lys and copy its NZ-HZ[123] group and use that.  gmx
> >> >>>> insert-molecules -nmol 300 will give you a box of 300.
> >> >>>>
> >> >>>> -Justin
> >> >>>>
> >> >>>>
> >> >>>>
> >> >>>>>  Sent with Mailtrack
> >> >>>>> <https://mailtrack.io/install?source=signature&lang=en&refer
> >> >>>>> ral=cy16f01.dilip at nitk.edu.in&idSignature=22>
> >> >>>>>
> >> >>>>> On Fri, Jan 6, 2017 at 11:01 AM, Alex <nedomacho at gmail.com>
> wrote:
> >> >>>>>
> >> >>>>> Google "bf3 rcsb" > third result from the top
> >> >>>>>
> >> >>>>>> https://www3.rcsb.org/ligand/BF3 > download cif file
> (view/download
> >> >>>>>> on
> >> >>>>>> the right) > open in pymol > save as pdb
> >> >>>>>>
> >> >>>>>> Alex
> >> >>>>>>
> >> >>>>>>
> >> >>>>>> On 1/5/2017 10:20 PM, Dilip H N wrote:
> >> >>>>>>
> >> >>>>>> I want to do a simulation of BF3 molecule..
> >> >>>>>>
> >> >>>>>>> how can i create a pdb file of BF3 molecule..??
> >> >>>>>>> is there any softwares for creating a .pdb files ..??
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>> --
> >> >>>>>>>
> >> >>>>>> Gromacs Users mailing list
> >> >>>>>>
> >> >>>>>> * Please search the archive at http://www.gromacs.org/Support
> >> >>>>>> /Mailing_Lists/GMX-Users_List before posting!
> >> >>>>>>
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> >> >>>>>>
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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.
> >> >>>>>>
> >> >>>>>>
> >> >>>>>>
> >> >>>>>
> >> >>>>>
> >> >>>>> --
> >> >>>> ==================================================
> >> >>>>
> >> >>>> Justin A. Lemkul, Ph.D.
> >> >>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >> >>>>
> >> >>>> Department of Pharmaceutical Sciences
> >> >>>> School of Pharmacy
> >> >>>> Health Sciences Facility II, Room 629
> >> >>>> University of Maryland, Baltimore
> >> >>>> 20 Penn St.
> >> >>>> Baltimore, MD 21201
> >> >>>>
> >> >>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> >>>> http://mackerell.umaryland.edu/~jalemkul
> >> >>>>
> >> >>>> ==================================================
> >> >>>>
> >> >>>> --
> >> >>>> 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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> or
> >> >>>> send a mail to gmx-users-request at gromacs.org.
> >> >>>>
> >> >>>>
> >> >>>
> >> >>>
> >> >>>
> >> >> --
> >> >> ==================================================
> >> >>
> >> >> Justin A. Lemkul, Ph.D.
> >> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >> >>
> >> >> Department of Pharmaceutical Sciences
> >> >> School of Pharmacy
> >> >> Health Sciences Facility II, Room 629
> >> >> University of Maryland, Baltimore
> >> >> 20 Penn St.
> >> >> Baltimore, MD 21201
> >> >>
> >> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> >> http://mackerell.umaryland.edu/~jalemkul
> >> >>
> >> >> ==================================================
> >> >> --
> >> >> 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.
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > With Best Regards,
> >> >
> >> > DILIP.H.N
> >> > Ph.D Student,
> >> > Research Scholar,
> >> > Department of Chemistry,
> >> > National Institute of Technology-Karnataka,
> >> > Surathkal, Mangaluru - 575025.
> >> >
> >>
> >>
> >>
> >> --
> >> With Best Regards,
> >>
> >> DILIP.H.N
> >> Ph.D Student,
> >> Research Scholar,
> >> Department of Chemistry,
> >> National Institute of Technology-Karnataka,
> >> Surathkal, Mangaluru - 575025.
> >> --
> >> Gromacs Users mailing list
> >>
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> >> posting!
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> >>
> > --
> > Gromacs Users mailing list
> >
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>
>
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