[gmx-users] Regarding gromacs commands..

[Justin Lemkul]

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&referral=cy16f01.dilip@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 ..??
>>>>>
>>>>>
>>>>>
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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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>> 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

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