Hi,
I am trying to solvate a protein that has a probe attached to a cysteine
residue and includes one crystal water molecule. The leap input file I am
using is included below. Basically, when I try to solvate the system with
the crystal water included in the initial pdb, I get the message
"ContainerCenterAt(): Skipping atom w/ unknown position: O:O" and the system
does not solvate properly (the number of water residues that leap adds
is 169969). If I try removing the crystal water, solvateOct works fine, and
solvateOct also works without problems on the protein without the probe on
the cysteine residue. Please advise!
source /usr/local/amber/amber10/dat/leap/cmd/leaprc.gaff
source /usr/local/amber/amber10/dat/leap/cmd/leaprc.ff03
loadamberparams /nfs/01/osu6030/libs/CY3.frcmod
loadOff /nfs/01/osu6030/libs/CY3.lib
loadamberparams /nfs/01/osu6030/libs/linkers/LK5.frcmod
loadOff /nfs/01/osu6030/libs/linkers/LK5.lib
loadamberparams /nfs/01/osu6030/libs/TAMs/4S2.frcmod
loadOff /nfs/01/osu6030/libs/TAMs/4S2.lib
loadamberparams /nfs/01/osu6030/libs/linkers/linktoCYS.frcmod
p = loadpdb test.pdb
check p
set p head p.63.SG
b = sequence {4S2 LK5 p}
check b
addions b Cl- 0
solvateOct b TIP3PBOX 8
savepdb b test.pdb
saveamberparm b test.prmtop test.inpcrd
quit
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Received on Mon Apr 11 2011 - 13:30:04 PDT
