[gmx-users] sep and tpo

[Justin Lemkul]

On 2/4/16 9:06 AM, Mehreen Jan wrote:
>
>
>
>
>
>   i just make changes in  gromacs 4.5.5>share>top>gromacs43a1.ff
> step of command i performed :
>> pdb2gmx -f protein.pdb -p protein.top -o protein.gro
>>
>> from list select the force field
>> select 9    which is GROMOS96 43a1 force field
>> select the water model:
>> 1    SPC simple point charge
>> then error message
>> fatal error:
>> residue SEP /TPO not found in residue topology database
>

Clearly this isn't working and you're not making the right changes (or you don't 
have sufficient permissions to alter those files).

I'm not going to continue to repeat myself with the same advice.  If you want 
free help, take the suggestions you've been given.  The force field you need is 
already built.  Use it.

-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

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