[gmx-users] Regarding gromacs commands..

[Dilip H N]

Sir, i want to run an simulation of 300 molecules of ammonia...
how can i proceed with it..??
can u please help me out....



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