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

From: Vlad Cojocaru (
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 ..


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 ../
> ambercoor ../s_comp1.crd
> outputname s_comp1_min
> exclude scaled1-4
> 1-4scaling 0.833333
> where 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.

Dr. Vlad Cojocaru
Heidelberg Institute for Theoretical Studies
Molecular and Cellular Modelling Group
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
Amtgericht Mannheim / HRB 337446
Managing Directors: Dr. h.c. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter (

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