Hi I was trying to do a GB minimization on a unnatural
compound. The force parameters were generated with
amber7 antechamber. Here is the error I got:bad atom
type: c1. By the way if I use the normal approach,
everything is fine.
Eric
GB input file:
cat <<eof>gbin
minimize structure
&cntrl
imin=1, maxcyc=100,
cut=300.0, igb=2, saltcon=0.2, gbsa=1,
ntpr=10, ntx=1, ntb=0,
&end
keep all atoms frozen
5.0
RES 1 219
END
END
eof
sander -O -i gbin \
-c 4bound.crd -p 4bound.top -ref 4bound.crd -o
4bound.min.out -r 4bound.rst
Normal mini.in:
cat <<eof > mdin_mini
minimize structure
&cntrl
imin=1, maxcyc=200,
ntpr=20, ntb=0, nsnb=999999,ntmin=2
&end
eof
sander -O -i mdin_mini \
-c 4bound.crd -p 4bound.top -o mini.out -r mini.rst
__________________________________________________
Do you Yahoo!?
Yahoo! Mail Plus – Powerful. Affordable. Sign up now.
http://mailplus.yahoo.com
Received on Sun Nov 24 2002 - 17:05:59 PST
