On Thu, Sep 10, 2015 at 6:41 AM, Eiros Zamora, Juan <
j.eiros-zamora14.imperial.ac.uk> wrote:
> Hi Jason,
>
> Thanks for your help. You’re right, the topology file was obtained some
> months ago using the parmed.py of AmberTools 14 to strip the waters out of
> the topology file that was used for MD production. I’ll try and look for
> the original one and make the proper changes with the newer version of
> parmed.py
>
In that case, try the script that I attached -- it should be a quick fix:
===
from chemistry.amber.readparm import AmberFormat
import sys
parm = AmberFormat(
sys.argv[1])
parm.parm_data['ATOMIC_NUMBER'] = parm.parm_data['ATOMIC_NUMBER'][:7425]
parm.write_parm(sys.argv[1])
===
Save that file to something like "fixparm.py" and then execute it via:
python fixparm.py <prmtop>
where <prmtop> is your topology file. This should fix your prmtop to have
only the correct number of atomic number entries.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 10 2015 - 06:00:04 PDT
