AMBER Archive (2002)

Subject: atom type not recognized by GB

From: eric hu (erichu_linux_at_yahoo.com)
Date: Sun Nov 24 2002 - 19:05:59 CST

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

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