Dear Prof.Case
Thanks a lot for your help again. Atoms 9223 and 9224 are the hydrogen atoms of the same water molecule.Following your comments, I checked my PDB file carefully , then I found a problem . The first step is the building of residues. I created the new Lib files for my residues which coordinate to the metal ion.The I using the script <......saveamberparm xxx xxx.prmtop xxx.inpcrd
savepdb xxx xxx.pdb>
to creat the top ,crd and pdb file. After doing this,the pdb file seems ok, it looks like :
ATOM 9223 H1 H2O 578 2.818 -3.196 6.735 1.00 0.00
ATOM 9224 H2 H2O 578 3.141 -1.732 6.953 1.00 0.00
ATOM 9225 O H2O 578 3.450 -2.615 7.160 1.00 0.00
TER
but when I use the order: ambpdb -p xxx.prmtop<xxx.inpcrd>xxx.pdb & ,this PDB displays like :ATOM 9223 H1 H2O 578 47.112 46.701 54.456
TER
ATOM 9224 H2 H2O 578 47.436 48.165 54.674
TER
ATOM 9225 O H2O 578 47.744 47.282 54.881
TER
The whole water molecule 578 was divided by three blocks ,I think it is the reason that caused the partition shake error,Could you tell me how to solve this ? Thank you very much !
At 2010-10-12 11:36:27，case <case.biomaps.rutgers.edu> wrote:
>On Tue, Oct 12, 2010, xuemeiwang1103 wrote:
>
>> Thanks a lot for your comments. There is a metal ion in my protein
>> sysytem.It tetracoordinated to three residues as well as one water
>> molecule.The number 9223 and 9224 is the H atom in the water
>> molecule which bonded to the metal ion. I used the bonded model
>> in Amber. The parrel simulation runs well during the heating
>> process,but when I run the MD in the NPT,the error happens.
>
>Can you be a little more specific? Are atoms 9223 and 9224 both H atoms in
>the same water molecule? Are they in the same residue? Sander should not
>be splitting atoms in the same residue up among processors (although it is not
>clear whether you are running sander or pmemd. Also which version?)
>
>It is indeed odd that the partition failure happens with NPT and not NVT.
>I assume(?) you used the same number of processors for each. Maybe answers
>to the questions above will help, but you will probably have to post your
>prmtop and coordinate files in order for someone here to try to be able to
>reproduce the problem.
>
>...thx...dac
>
>
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Received on Tue Oct 12 2010 - 01:30:05 PDT
