[gmx-users] Regarding gromacs commands..

[Justin Lemkul]

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

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> 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 ..??
>>>
>>>
>>>
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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

==================================================