[gmx-users] Regarding gromacs commands..

Mon Jan 9 18:48:04 CET 2017

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
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> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>> ==================================================
> >>>>
> >>>> 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
> >>>>
> >>>> ==================================================
> >>>>
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> >>>>
> >>>
> >>>
> >>>
> >> --
> >> ==================================================
> >>
> >> 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
> >>
> >> ==================================================
> >> --
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> >>
> >
> >
> >
> > --
> > 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.
> --
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