From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Thu Feb 08 2018 - 07:32:26 CST
Hi,
I am not sure how NAMD deals with amber generated trajectory files and
experts may advise something for that. Generally NAMD reads binary
traj files (e.g. dcd files) using "coorfile" option as it is said in
*http://www.ks.uiuc.edu/Research/namd/2.9/ug/node9.html
<http://www.ks.uiuc.edu/Research/namd/2.9/ug/node9.html>. *
In your script, you have read both your initial coordinate file and
traj file with " coordinates " option which I guess work with readable pdb
formats. Your error clearly says that your string is empty. So neither
your initial coordinates nor the traj file has been read I think. So you
can try reading a pdb file as inital coordinate file and use 'coorfile'
option to read your binary trajectory.
On Thu, Feb 8, 2018 at 1:02 PM, Jeyaram R A <ra.jeyaram_at_vit.ac.in> wrote:
> Dear NAMD users,
>
>
> I want to calculate pair interaction energy by using amber generated
> parameters and coordinates, while executing the script it
> shows the following error.
>
>
> *script:*
>
> # pair interaction energy calculation
> # Amber generated top and crd file is used
> amber yes # Specify this is AMBER force field
> # amber generated top and crd file
> parmfile 1.top # Input PARM file
> coordinates 1.crd # Input coordinate file
> structure md.nc
>
> # approximations
> timestep 2.0
> cutoff 8.0
> switchdist 7.0
> pairlistdist 10.0
> exclude scaled1-4
> 1-4scaling 0.83333 # 1/scee where scee in amber is 1.2
> # Atoms in group 1 have a 1 in the B column; group 2 has a 2.
> pairInteraction on
> pairInteractionFile pair.pdb
> pairInteractionCol B
> pairInteractionGroup1 1
> pairInteractionGroup2 2
>
> # First frame saved was frame 500.
> set ts 500
>
> coordinates open NetCDF md.nc
>
> # Read all frames until nonzero is returned.
> while { ![coordinates read] } {
> firstTimestep $ts
> run 0
> incr ts 500
> }
> coordinates close
>
>
>
> *error: *
>
>
> Reason: FATAL ERROR: can't use empty string as operand of "!"
> while executing
> "while { ![coordinates read] } {
> firstTimestep $ts
> run 0
> incr ts 500
> }"
> (file "pair.inp" line 29)
>
> Charm++ fatal error:
> FATAL ERROR: can't use empty string as operand of "!"
> while executing
> "while { ![coordinates read] } {
> firstTimestep $ts
> run 0
> incr ts 500
> }"
> (file "pair.inp" line 29)
>
> Aborted (core dumped)
>
>
> Thanks in advance
>
>
>
>
>
>
>
>
-- Souvik Sinha Research Fellow Bioinformatics Centre (SGD LAB) Bose Institute Contact: 033 25693275
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