AMBER Archive (2002)

Subject: igb=2,gbsa=1,antechamber,bad atom type

From: Jianhui Wu (wujih_at_BRI.NRC.CA)
Date: Fri May 17 2002 - 14:20:14 CDT

Dear Amber users,

My sander parallel version is now running on our SMP Linux cluster. I
am grateful for the help from Drs. David Case, Tru Huynh, Stéphane
Teletchéa and Joffre Heredia Rodrigo.

Here, I encounter a problem with continnumn model igb=2, gbsa=1 when the
top and crd files are originated from antechamber module.

(a) ETH.prepi file of ethane was prepared using antechamber.
    Then, parmchk is used to generate frcmod file.
(b) ETH.top and ETH.crd (source leaprc.gaff) was prepared by tleap.

(c) If I only use igb=2 to run mm or md, things are fine. However, the
combination of 'igb=2, gbsa=1 or igb=1, gbsa=1' will not run. It just
complain 'bad atom type: c3'. This happened to other small molecule I
tested too.

Here is what my input file look like:
*******************************************************************
cat <<eof > mdin
  minimize structure
 &cntrl
   imin=1, maxcyc=100,
   cut=300.0, igb=2, saltcon=0.2, gbsa=1,
   ntpr=10, ntx=1, ntb=0,
   ntr=1,
 &end
  keep all atoms frozen
  5.0 RES 1 END END eof sander -O -i mdin \ -c ETH.crd -p ETH.top -ref
ETH.crd -o ETH.min.out -r ETH.rst &
*********************************************************************

It works fine for free protein and have problem with small molecule
(ligand). Can someone give me a hand?

Thanks a lot,

Jian Hui Wu
Lady Davis Institute