Your errors look weird; I haven't seen any like that before that I can
recall. Can you attach the PDBs you tried using?
On Thu, Apr 14, 2011 at 8:11 AM, Hashem Taha <htahaphd.gmail.com> wrote:
> Any suggestions???
>
> On Tue, Apr 12, 2011 at 8:56 PM, Hashem Taha <htahaphd.gmail.com> wrote:
>
> > 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 14 2011 - 08:30:04 PDT
