[AMBER] problems with paramfit

From: Marek Maly <marek.maly.ujep.cz>
Date: Thu, 24 Jul 2014 23:56:00 +0200

Dear all,

I just wanted to do some "revision" ff parameters fitting using the
paramfit from the
actual Amber14. When I tried to use this actual paramfit version for FIT
I realized that the value of the constant K clearly written in the control
(K=-196.792733) was not read in and instead default value of K (i.e.
0.0000) is
used and written in the screen.
So I decided to use recommended wizard to create control file (however in
case of
the older paramfit versions I never had problem with control file created
by hand).

Unfortunately the wizard failed exactly in the step where it had to read
K constant value,
please see below. I verified this behavior on two different HW platforms.

So it seems that the actual paramfit version (at least the my OpenMP
version) has some problems
in reading of the floating point numbers (from the file and as well from
the screen (wizard)).

I tried here to change the number of cores (using OMP_NUM_THREADS) from 8
to 1 (for the wizard work) but this did not helped. I would be very
grateful for any useful suggestions which could help me to
solve this problem.

I am using Amber14 with the patches up to 3 (in case of AT up to 6).
My OS is CentOS release 6.5 (2.6.32-431.el6.x86_64), I used gnu compilers
to compile Amber14 ( gcc version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC) ).
I did not recognize any other problems (e.g. durin MD simulation) and all
tests which are recommended part of the Amber14 installation proceeded

   Thank you in advance for the help,

         Best wishes,


! Setting verbosity to medium.

                 * AMBER Bond Angle and Dihedral Parameter Optimiser *
                 * *
                 * v3.0.0 *
                 * *
                 * Written by: *
                 * Robin Betz (2011) *
                 * Ross Walker (2004) *
                 * The Walker Molecular Dynamics Lab *
                 * University of California, San Diego *
                 * La Jolla, California, 92092 *
                 * USA *

                                 Execution started at:
| Thu Jul 24 23:31:16 2014

| Running OpenMP version of code using 1 processors

| Random seed = 1406237476

Enter a job control filename to save settings as, or hit enter
> control.in
Saving job control settings as "control.in"

How many input structures do you have?

Which format is your coordinate file in?
         1) Trajectory (.mdcrd,.inpcrd)
         2) Restart (.rst, .restart)

What type of job do you want to run?
         1) Create input files for quantum program
         2) Set which parameters to fit
         3) Conduct a fit

Which parameters would you like to fit?
         1) Defaults (see manual)
         2) Load list from file
         3) K only
> 2
Enter file name:
> parameters.in
Enter the initial value for K:
> -196.792733
Error: signal 11:
[mara.node25 04_FIT]$

Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
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Received on Thu Jul 24 2014 - 15:30:02 PDT
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