Dear Amber users and Developers,
I have done first
minimization by sander keeping the protein fixed. Then I did all atom
minimization by pmemd.cuda. After that I am trying to heat the system
from 0K to 300K by pmemd.cuda. Here run is stopping giving a message.
The message is-
"Hydrogen atom 4103 appears to have multiple bonds to atoms 4101 and
4103 which is illegal for SHAKEH.
Exiting due to the presence of inconsistent SHAKEH hydrogen clusters."
On seeing this I check the position of atoms 4103 and 4101. They are
oxygen and hydrogen atoms of a water molecule. Distance between them
is 0.99 angstrom and it is O-H single bond distance in water. Yet the
above message is coming. When I run the same in sander, then there is
no problem. I want to run in pmemd.cuda. Where is the problem? Please
help me.
Sanjib Paul
Indian Institute of Technology,Kharagpur,
India
On 1/24/13, Sanjib Paul <sanjib88paul.gmail.com> wrote:
> Dear Amber Users and Developers,
> I am working on
> HCA II taking 2cba.pdb. It does not have two N-terminal residues. So,
> to get proper residue number I attach two N-terminal residues by
> SWISS-PDB VIEWER. Unfortunately there have been some unusual bonds
> between residue 1 and some crystal waters(resid 270,279,295). I
> thought after minimization structure would be good. When I run
> pmemd.cuda to minimize there is no change in that portion. VDW
> energies are too large that they are not coming. But if I run sander
> the unusual bonds are broken and VDW energy values are coming from the
> NSTEP = 50. (ntpr = 50). So, starting with sander can I continue my
> rest of simulation with pmemd.cuda?
>
> Sanjib Paul
>
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Received on Thu Jan 24 2013 - 04:00:02 PST
