[AMBER] Issue with solvateOct for a large system

From: <benedikt.diewald.fau.de>
Date: Wed, 25 Jan 2017 16:03:34 +0100

Hi all,

I just discovered an issue with the tleap command solvateOct. I tried to
solvate a rather large system with about 2400 residues in a 10 Angstrom
water box. On visual inspection I realized that parts of the molecule are
located outside of the cell, as well as a few ions, used to neutralize the
While browsing through the mailing lists archive I came upon a very
similar case from 2012:
"Centering a multimeric protein with solvateOct"
I believe this to be the same problem so I tried the suggested solution
(connecting all monomers with bonds), however, without any success.

My use of SolvateOct is this:
solvateOct com TIP3PBOX 10.0

For additional information I attached the Input file and the leap.log to
this email.

Together with the older case, this issue has been observed in AMBER
versions 12, 14, and 16.

- Benedikt

AMBER mailing list

Received on Wed Jan 25 2017 - 07:30:02 PST
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