Hi Ben,
Attached is the original bcl file (prot1.pdb_large_60hrs.bcl) that got stuck
during execution.
Later, I modified the residue names in accord with standard residues and now
the program is terminating with segmentation fault. Attached are the
modified .bcl and corresponding log file. Please have a look into it and
suggest a solution to this problem.
Thanks,
Manish
-----Original Message-----
From: Ben Roberts [mailto:ben.roberts.geek.nz]
Sent: Tuesday, May 03, 2011 5:20 PM
To: AMBER Mailing List
Subject: Re: [AMBER] MCPB problem
Hi Manish (and Hashem),
On 3/5/2011, at 5:13 p.m., Manish wrote:
> Thanks for your suggestions, there was some progress when I copied the
> standard residues. But now I'm getting following error:
>
> <snip>
In addition to the problem with the proper residue templates, protonation
and other parts of MTK++ are known to have bugs in them, that sometimes
manifest as infinite loops (like the 60-hour wait you described). I haven't
heard of this more recent problem. Could you please send your revised BCL
file too, and I (and/or other MTK++ developers) will take a look at it and
get back to you.
Regards,
Ben
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Received on Wed May 04 2011 - 08:30:03 PDT
