Re: FATAL ERROR: Setting parameter constraints from script failed!

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Thu Jan 08 2009 - 11:14:24 CST

Hi Trang,

I find a simple way to do this is to set up a constraint file with the
force constants set to 1.0 (usually in the beta column). Let's say
that I want to start the constraints (restraints) at 5.0 kcal/mol/A^2.
I use the following script at the end of my file to gradually decrease
the constraints:

constraints on
consref ../xxx_protrestraint.pdb
conskfile ../xxx_protrestraint.pdb
conskcol B

#protocol

set k_init 5.0

for {set i 0} {$i <= 10} {incr i 1} {
set ck [expr {$k_init - $i*0.5}]
constraintScaling $ck
run 25000
}

This protocol assumes that you're restraining all of your atoms with
the same force and that you want to decrease them uniformly.

Josh

On Jan 8, 2009, at 8:58 AM, Axel Kohlmeyer wrote:

> On Thu, 8 Jan 2009, Do Nhu Trang wrote:
>
> DNT> Dear all,
>
> dear trang,
>
> DNT> I would like to perform a simulation with restraints released
> gradually. I
> DNT> want to control several phases in one configuration file. The
> procedure I
>
> if i remeber correctly, NAMD doesn't handle this scenario very
> gracefully. you better be using multiple input files. there is
> next to no gain from having this in one script anyways.
>
> cheers,
> axel.
>
>
> DNT> have done is the following:
> DNT>
> DNT> 1. turn on the constraints
> DNT> 2. specify the reference pdb file together with force constant
> DNT> 3. run for a number of timesteps
> DNT> 4. turn off the constraints
> DNT> 5. turn on again with another reference pdb file and force
> constant
> DNT> 6. run for another number of timesteps
> DNT> ...
> DNT> The detail script of this part is attached below. After running
> for the
> DNT> first number of steps (20000 in this case), NAMD stops running
> and reports
> DNT> this following error:
> DNT> "TCL: Setting parameter constraints to off
> DNT> FATAL ERROR: Setting parameter constraints from script failed!"
> DNT>
> DNT> I found the similar problem reported by Marc vander Kamp a long
> time ago
> DNT> http://www-s.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1095.html
> DNT> but there is still no reply to this message. I would like to
> ask Marc if he
> DNT> could already solve this problem, and I also need help from all
> NAMD users.
> DNT>
> DNT> Many thanks.
> DNT> Trang.
> DNT>
> DNT> #####################
> DNT>
> DNT> constraints on
> DNT> consref K_18_restrained_5.pdb
> DNT> conskfile K_18_restrained_5.pdb
> DNT> conskcol B
> DNT> run 20000;
> DNT> constraints off;
> DNT>
> DNT> constraints on;
> DNT> consref K_18_restrained_3.pdb;
> DNT> conskfile K_18_restrained_3.pdb;
> DNT> conskcol B;
> DNT> run 5000;
> DNT> ..........
> DNT>
>
> --
> =
> ======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
> www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =
> ======================================================================
> If you make something idiot-proof, the universe creates a better
> idiot.
>

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
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