[AMBER] Solvents that are not in a list.

From: Sharapa <dmitriy.sharapa.fau.de>
Date: Thu, 30 Jul 2015 13:16:55 +0200

Dear Amber users,

I am new in amber and i want to make MD simulation of small organic
molecule in a solvents that are not in a list of AMBer (neither in
Manchester Bryce group database, precisely i am interested in toluene,
THF and benzonitrile). As far as i understood trying to describe the
solvent with leap parameters as for single molecule should be incorrect
due to wrong description of bulk interaction. I am afraid that
parametrisation of new solvents is too compicated for my skills. On a
http://virtualchemistry.org i found some files that looks rather
usefull: GAFF topology and GAFF liquid structure. I am looking on GAFF
while i already had to parametrise Si atom that is in molecule and i
made it in GAFF forcefield, also i hope that its good enough for
describing pi-stacking that should have place at my molecule of interest.
What can/should i do in this situation?

Thanks in advance,

AMBER mailing list
Received on Thu Jul 30 2015 - 04:30:03 PDT
Custom Search