[gmx-users] Regarding gromacs commands..
jalemkul at vt.edu
Fri Jan 6 19:46:02 CET 2017
On 1/6/17 2:24 AM, Dilip H N wrote:
> 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
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 group and use that. gmx insert-molecules -nmol 300 will
give you a box of 300.
> Sent with Mailtrack
> 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
>> 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 ..??
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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
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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