AMBER Archive (2008)

Subject: Re: AMBER: problems with sleap

From: David A. Case (
Date: Mon Jun 16 2008 - 10:48:42 CDT

On Thu, Jun 05, 2008, Alan wrote:

> Sorry, later I noticed I was not being clear. I guess it because I so
> annoyed with 'basic_string::substr' that I didn't pay attention the rest.
> But here goes in attach 2 pdbs.
> dmp.pdb (from pdb 1BVG)
> AAA.pdb (created with pymol)
> mol2 files can be generated with babel.
> I also noticed that sleap might not like sybyl atom definitions, only
> gaff/amber atom types, is that right?

To make a prmtop, you need gaff or amber atom types, for sure.

We think we have the problem fixed (i.e. you can set fastbld to "on", and load
and save dmp.pdb), with no "substr" messages. The fix will be incorporated
into version 1.1 of AmberTools, which will be announced soon. [There have
been lots of changes to sleap since version 1.0, so trying to provide
individual patches seems likely to cause more harm than good.]

Thanks again for reporting this...dac

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