I have tried HOH, WAT and TP3 for the residue name for the crystal water,
but no luck. The odd thing that I am confused about is that when the crystal
water is present without the probe attached to cysteine residue (i.e the
native protein), the solvation occurs with no problem, and when the probe is
attached and the crystal water is removed, it also works. So, I'm really not
sure what the problem is. I've attached the leap.log file
On Tue, Apr 12, 2011 at 9:20 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> >
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- application/octet-stream attachment: leap.log
Received on Tue Apr 12 2011 - 19:30:07 PDT
