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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Received on Thu Apr 14 2011 - 08:30:03 PDT
