From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Oct 07 2015 - 16:14:12 CDT
Currently, with VMD it is straightforward building pure proteins in
CHARMM-compatible OPLS-AAM for NAMD. However, this is seldom enough with
real systems. Who can kindly answer a few questions?
(1) Are there top/par repositories for small molecules in CHARMM-compatible
OPLS-AAM ff other than those provided in MacKerrel toppar_c36_aug15.tgz
(2) Is any non-commercial tool of the type of CGenFF or whichever other
type, for building the ff for small molecules in CHARMM-compatible OPLS-AAM?
(3) Is any guideline to adapt the CHARMM ff of small molecules, derived
with CGenFF or other tool, to CHARMM-compatible OPLS-AAM?
(4) If 1-3 receives a "no", is any experience about using with NAMD a mix
of ff, i.e., OPLS-AAM for the protein/water/NA+/Cl- and CHARMM for organic
thanks for advice
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