AMBER Archive (2008)

Subject: Re: AMBER: problems with sleap

From: Qi Zhang (qizhang_at_mbi.ucla.edu)
Date: Mon Jun 16 2008 - 06:46:26 CDT

Thanks,

Qi

On Jun 16, 2008, at 8:48 AM, David A. Case wrote:

> 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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