[gmx-users] Regarding gromacs commands..

Mon Jan 9 19:15:53 CET 2017

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
>> >>>>>>
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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
>> >>>>
>> >>>> ==================================================
>> >>>>
>> >>>> --
>> >>>> Gromacs Users mailing list
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>> >>>> 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
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>> >> 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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>>
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