Hi Manish,
We will need the following files:
prot1.pdb_settings.bcl and NAME_fixed.pdb
to reproduce the problem locally.
Regards,
Martin.
On 4 May 2011, at 16:22, Manish wrote:
> 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
>
> --
> For greater security, I support S/MIME encryption.
>
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Received on Wed May 04 2011 - 09:00:02 PDT
