[gmx-users] New atom definition

[Justin Lemkul]

On 9/18/15 12:20 AM, Maryam Kowsar wrote:
> Thaks justin!
> I did it several times and it worked. But now when i want to add some
> neutral gas or heavy atoms it stops me with the error that the atom is not
> defined. I dont know where i make a mistake.
>

Neither does anyone here, because you haven't provided any useful information 
about the problem.  You need to tell us (1) exactly what you're doing - what 
you've added and how you've done it and (2) exactly what the error message is - 
copied and pasted from the terminal, not re-typed or interpreted.

-Justin

> On Friday, September 18, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/17/15 3:08 PM, Maryam Kowsar wrote:
>>
>>> Dear all,
>>>
>>> I want to use some atoms that are not implemented in gromacs. If i even
>>> make a .gro file, making a topology is a problem. What should i do?
>>>
>>>
>> Derive parameters in a manner consistent with the desired force field and
>> add all necessary bonded and nonbonded parameters to ffbonded.itp and
>> ffnonbonded.itp.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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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-- 
==================================================

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

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