Based on your test.pdb, I'm actually surprised that it ever worked. The
hydrogens all have weird names that don't conform to the PDB standards
(2HB, 3HB, 1HG2, etc.) where they should be (HB2, HB3, HG12, etc.)
Try getting rid of all hydrogens from your PDB files and running leap
again. You can remove hydrogens with many tools, including reduce, sed, or
grep. My personal suggestion is reduce.
reduce -Trim test.pdb > test_noh.pdb
leap should add the hydrogen atoms back for you. See if this helps fix your
problems. Based on the files you gave me (just the PDB really), I have no
idea how you're getting the errors you're reporting.
Good luck,
Jason
On Thu, Apr 14, 2011 at 8:37 AM, Hashem Taha <htahaphd.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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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 - 09:30:08 PDT
