Dear Amber users,
I'm trying to do a little TI with Crambin. I want an extra electron to
transfer from one phenylalanine residue to a thyrosine residue.
Therefore I modified these residues charges in the mol2 files in such a
way that the additional electron is located in the phenyl ring.
The needed frcmod and lib files where done following the tutorials.
The first run I did was interrupted because of SHAKE errors, therefore I
turned SHAKE off. With that, the simulations ended whith the following
errors:
SanderBomb in subroutine nonbond_list
Nonbond list overflow
(calcuation interrupted here)
and
SanderBomb in subroutine nonbond_list
volume of vcell too big, too many subcells
list grid of memory needs to be reallocated, restart sander
(calcuation interrupted here)
and a mention of "vlimit exceeded" after nearly every calculation step.
This seemed to prevent the calculation of the dV/dL value.
Only the calculations for lambda=0 and lambda=1 could be done correctly.
I then checked the pdb after minimization and saw that the Crambin
lacked one bond in the backbone, which to me seems to be the reason to
the first SanderBomb error.
The original pdb I used was taken from the protein database and seemed
to be perfectly okay.
I would highly appreciate any of your ideas to bring my calculation on a
successful way.
Best regards
Anna
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Received on Tue Sep 11 2012 - 02:30:03 PDT
