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
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On Sat, Jan 7, 2017 at 12:15 AM, Justin Lemkul <jalem...@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
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On Fri, Jan 6, 2017 at 11:01 AM, Alex <nedoma...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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