Re: namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase

From: Vlad Cojocaru (Vlad.Cojocaru_at_h-its.org)
Date: Wed Mar 31 2010 - 07:02:07 CDT

Dear Peter,

I did not have the time to further test new CVS codes but if you still
have the problem with the newest CVS codes .. I am afraid that the
problem is not fixed yet.
I post my reply to the list as well maybe there are some updates from
the NAMD developers on this .. Of course, this problem is a very
important one for everybody who is using NAMD with AMBER ff ..

Cheers
Vlad

Peter Schmidtke wrote:
> Dear Vlad,
>
> I saw your posts on the namd mailing list and wondered if you finally
> solved the problem, I have the same right now and I did not find any follow
> up of the problem on the namd mailing list.
> The amber ff part of my conf file looks like this :
>
> amber on
> parmfile ../s_comp1.top
> ambercoor ../s_comp1.crd
> outputname s_comp1_min
> exclude scaled1-4
> 1-4scaling 0.833333
>
> where s_comp1.top is a amber topology, and the crd file is an amber
> coordinate file. Like in your case it yields a segmentation fault during
> the starting phase.
>
> Thanks in advance for your help
>
> Best regards.
>
>
>

-- 
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Dr. Vlad Cojocaru
Heidelberg Institute for Theoretical Studies
HITS gGmbH
Molecular and Cellular Modelling Group
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69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]h-its.org
http://projects.villa-bosch.de/mcm/people/cojocaru/
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