Dear Amber Developers and Users,
I am attempting to use paramfit from AmberTool12 to fit some dihedral
parameters missing from the GLYCAM forcefield.
I am using two small molecules (methylmethoxyacetate and methyl
tetrahydropyran-2-carboxylate) to fit terms for Os-Cg-C -O and Os-C -Cg-Os.
As the paramfit tutorial mentions, directionality of the dihedral terms
should be irrelevant (i.e. Os-Cg-C -O should be the same as O -C -Cg-Os),
but that does not appear to be the case:
When I run paramfit with the parameter file generated from one of the two
molecules, I get the following error in the output file:
Reading prmtop file list: prmtops_list
Reading prmtop file : methylmethoxyacetate.prmtop
Reading prmtop file : methylTHP2carboxylate.prmtop
No match for dihedral O -C -Cg-Os term 0 in prmtop!
This would indicate to me that order does matter afterall. Additionally,
when I generate the parameter file from the two molecules, the dihedral
terms are not in the same order:
methylmethoxyacetate:
#V2 AUTO-GENERATED PARAMETER FILE - DO NOT MODIFY
#
# BOND INFORMATION:
#### BOND REQ KR ####
#
# ANGLE PARAMETERS:
#### ANGLE KT THEQ ####
#
# DIHEDRAL PARAMETERS:
#### DIHEDRAL TERM KP NP PHASE ####
O C Cg Os 0 1 1 1
O C Cg Os 1 1 1 1
O C Cg Os 2 1 1 1
Os C Cg Os 0 1 1 1
methyl tetrahydropyran-2-carboxylate:
#V2 AUTO-GENERATED PARAMETER FILE - DO NOT MODIFY
#
# BOND INFORMATION:
#### BOND REQ KR ####
#
# ANGLE PARAMETERS:
#### ANGLE KT THEQ ####
#
# DIHEDRAL PARAMETERS:
#### DIHEDRAL TERM KP NP PHASE ####
Os Cg C Os 0 1 1 1
Os Cg C O 0 1 1 1
Os Cg C O 1 1 1 1
Os Cg C O 2 1 1 1
It is not clear to me at which point the terms are defined or how to change
their order, so I am hoping someone can point me to a solution to my
problem - possibly this is a mistake I made in generating the prmtop files?
Thank you very much for your help!
-Sven
--
Sven Hackbusch
PhD Candidate
Department of Chemistry
University of the Pacific
<https://www.linkedin.com/pub/sven-hackbusch/53/639/aa8>
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Received on Tue Nov 22 2016 - 16:00:03 PST
