CY3.off and CY3.frcmod are attached! note that .lib is used in the leapin
file. I changed it to .off in order to attach it to this message (gmail
wouldn't let me send .lib files!)
On Thu, Apr 14, 2011 at 11:39 AM, Hashem Taha <htahaphd.gmail.com> wrote:
> sorry LK5.off is attached now!
>
>
> On Thu, Apr 14, 2011 at 11:37 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
>>> > >> > _______________________________________________
>>> > >> > AMBER mailing list
>>> > >> > AMBER.ambermd.org
>>> > >> > http://lists.ambermd.org/mailman/listinfo/amber
>>> > >> >
>>> > >>
>>> > >> _______________________________________________
>>> > >> AMBER mailing list
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>>> > >>
>>> > >
>>> > >
>>> > _______________________________________________
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>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>>
>>>
>>>
>>> --
>>> 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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- application/octet-stream attachment: CY3.off
Received on Thu Apr 14 2011 - 09:30:03 PDT
