AMBER Archive (2002)

Subject: Re: nmode segmentation fault

From: jim caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Thu Aug 08 2002 - 13:21:03 CDT

You need to save your minimized (sander) coordinates as
binary "ntxo=0" and read them in to nmode also as
binary "ntx =0".

On Thu, 8 Aug 2002 zhongh_at_umich.edu wrote:

> Dear AMBER users:
>
> I am trying to get the deltaH using nmode module in AMBER package for complex,
> protein and ligand, after several
> try, at first it said the memory is not enough. After I increased the sizes.h
> file and ran it again, it can go through the minimization step. However, when
> calculating the nmode step, it always gives me error message. At first the drms
> in both nmode_min.in and nmode.in is 0.00001. Then it tells me that the RMS
> gradient from input (after minimization) is bigger than the required 0.00001.
> Then I increase the drms in nmode.in to 0.00005. However, it gave me the core
> dump file. Another point I want to point out is that no matter I ran it in the
> formatted or unformatted form, it gave me the same result. THat means, the
> minimization step was always ok, but the nmode step was always not ok. The
> related .in file is attached as follows. By the way, the system is around 88
> amino acids to 99 amino acids.
>
> Can someone give me a hand? Thank you very much.
>
> Haizhen Zhong
>
> File in nmode_min.in
>
> minimization, saving coords in binary
> &data
> ntrun=4,
> nsave=2,
> ndiag=2,
> cut=95.0,
> nprint=100,
> drms=0.00001,
> maxcyc=100,
> bdwnhl=0.01,
> dfpred=0.1,
> scnb=2.0,
> scee=2.0,
> nvect=200,
> ntxo=1
> &end
>
> File of nmode.in
> &data
> ntrun = 1, nsave=2, ndiag=2, cut=95.0, ibelly=0, ntx=1,
> nprint=1, ioseen=0,
> drms = 0.00005, maxcyc=1, bdwnhl=1.1, dfpred = 0.1,
> scnb=2.0, scee=2.0, idiel=0,
> nvect=200
> &end
>
> log file
>
> Amber demo/crown_ether: normal mode analysis
>
> nmode: minimization of crown in vacuum:
> nmode: frequencies and thermodynamic analysis:
> Segmentation fault (core dumped)
>
>
>
>
>

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James W. Caldwell (voice) 415-476-8603
Department of Pharmaceutical Chemistry (fax) 415-502-1411
Mail Stop 0446 (email) caldwell_at_heimdal.ucsf.edu
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University of California
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