What is the residue name of the water in the PDB? I think it needs to
be 'WAT' for leap to recognize it as a water. Attaching your full leap
output may help to debug your problem further.
-Dan
On Mon, Apr 11, 2011 at 4:09 PM, Hashem Taha <htahaphd.gmail.com> wrote:
> 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 Tue Apr 12 2011 - 06:30:03 PDT
