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,
Dmitriy.
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Received on Thu Jul 30 2015 - 04:30:03 PDT
