Hi Martin,
> source leaprc.ff94
> gaff = loadamberparams gaff.dat
> loadamberprep PSB.prepin
> loadamberprep CH3.prepin
> mol = sequence { CH3 PSB }
This is the problem here. The sequence command just builds structures using
common templates it doesn't have any idea of ring planarity, stereo
chemistry etc.
You have two options here. The first option is not to worry about the
initial structure. Just try minimising the system and see if the structure
corrects itself. It probably will. if it doesn't you can try do some short
low temperature MD with a short time step (say 0.2fs) and then cool the
system down to 0 K. This will work where minimisation may fail since it will
allow you to move out of what is potentially a high energy minimum.
The second option is to build the starting structure outside of leap and
load in a pdb into leap instead of using the sequence command. I.e. you
could run a simple MM2 calculation or a small QM calculation on the system
and then convert the output file into a pdb. Then edit this pdb. Give the
various atoms their correct residue ids and then do:
loadamberprep PSB.prepin
loadamberprep CH3.prepin
mol = loadpdb my_molecule.pdb
This should then retain the structure from the pdb file rather than those
from the prepin file.
good luck...
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Apr 30 2006 - 06:07:11 PDT
