AMBER Archive (2005)

Subject: Re: AMBER: seg fault error in resp

From: Kateryna Miroshnychenko (kateryna_mirosh_at_ire.kharkov.ua)
Date: Wed Oct 26 2005 - 10:26:37 CDT

Dear Francois,

Thanks for your prompt reply.
> You changed the RESP source code (resp.f) to increase the number of molecules in
> the fit. Right ?
Yes, I just changed all the occurencies of maxq=500 to maxq=2000. I had
to do this because earlier I've had problem with max number of
centers(more than 500).

> I would 1st test RESP using the two aliases:
> alias resp1 'resp -O -i input1 -e espot -o output1 -p punch1 -q qout -t qout1 -w
> qwts -s esout'
> alias resp2 'resp -O -i input2 -e espot -o output2 -p punch2 -q qout1 -t qout2
> -w qwts -s esout'
>
> using simple RESP inputs involving a single molecule, conformation & orientation
> i.e. with nmol=1 and a single MEP in the espot file...
> Do you get also this error message with those very simple inputs ?
No, in the case of simple single molecule inputs everything is working
fine.
This problem arose when I was trying to establish how many
reorientations of alanine should be used to obtain charges
with accuracy of 0.001. I compared resp charges calculated for one
conformation using two different sets of 15 reorientations. The max
difference in q value was circa .005. Then I wanted to compare this
charges with charges calculated using maximum possible number of
reorientations(60 if only heavy atoms(5 in ala) are used) . Since the
number of all atoms in ala is 10, the total number of centers is 600.
Here the problem occured.
May be you can suggest any clever way to select particular
reorientations that will minimize the charge uncertanty.

Thanks in advance,
 Katya

********************************************
 Kateryna Miroshnychenko
post-graduate student
Department of Biological Physics,
Institute of Radiophysics and Electronics,
National Academy of Sciences of Ukraine,
Kharkiv, Ukraine
E-mail:kateryna_mirosh_at_ire.kharkov.ua
********************************************

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