(unknown charset) [AMBER] Issue with running sander

From: (unknown charset) 板垣哲彦 <itagaki08.gmail.com>
Date: Fri, 30 Mar 2012 21:37:21 +0900

Dear AMBER users and developers,

I performed sander for a protein in the free state, which
was a successful work.

But, for the complex with ligands, I detected the following
error message;

----------------------------------------


 vlimit exceeded for step 0; vmax = 29909.5926
 partition error in shake on processor 0
 this processor has atoms 1 through 9100
 atom 9098 is within this range
 atom 9101 is not within this range !


------------------------------------------

In the PDB-formatted file, there is a TER line between the
9100 and 9101 atoms, as follows, and it may lead the above
error, I think.

--------------------------------------------


 ATOM 9098 C15 L35 579 49.112 52.954 68.279
 ATOM 9099 H7 L35 579 48.964 51.593 69.965
 ATOM 9100 H8 L35 579 50.040 51.978 70.486
 TER
 ATOM 9101 H9 L35 579 48.089 50.908 70.547
 ATOM 9102 C16 L35 579 32.519 59.825 33.305


---------------------------------------------

L35 represents a ligand, which is not covalently bound to
the protein.

I can not see why sander gives us the above errors. If you
could let me know some instructions of this issue, I would
much appreciate it.


best regards,
Tetsuhiko
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Received on Fri Mar 30 2012 - 06:00:04 PDT
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