I have attached the test.pdb file as well as the frcmod and lib files for
4S2 and LK5.
On Thu, Apr 14, 2011 at 11:20 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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> > >>
> > >
> > >
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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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- application/octet-stream attachment: 4S2.off
Received on Thu Apr 14 2011 - 09:00:02 PDT
