Hi Amber Users,
I am doing MD of my protein bound with ligand and cofactor. The complex was
prepared well using antechamber and tleap modules (did not show any
error).*TIP3P
* water type was used to solvate the system. I minimized the protein complex
(*total :5320 atoms*) using steepest descent and conjugate gradient method (
*Total: 2500 and ncyc:1500*). It showed "Linmin Error" when it moved from
steepest descent to conjugate gradient. I searched for the error and found
it to be related to some coordinate overlap. To solve the problem, I
optimize my complex using Schrodinger and again prepare the protein complex
using tleap. This time it is not showing such error (no warning in the mdout
file) but still the job was killed at 1500 step. In mdout file also it is
not showing any warning.
I am confused whether I should ignore this and optimize my system using
increased number of steepest descent minimization and no conjugate gradient
steps? Suggest me what should I do?
Thanks,
Hirdesh
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Received on Wed Jan 19 2011 - 22:00:03 PST
