From: Sting (stg1979_at_emails.bjut.edu.cn)
Date: Tue Jun 06 2006 - 08:32:48 CDT
namd-lHi all:
I tried to compute the pair force using namd from a gromacs format trajectory(*trr). Following the user guide of namd,
I builded the configure file(see below),but when I ran,some error occured:
Info: GROMACS TOPO FILE TEQ2NO.top
Info: GROMACS COOR FILE ../avg_wild_TEQ_md.pdb
Required bondtype NL--H (function 2) not found.
------------- Processor 0 Exiting: Called CmiAbort -----------
And NL--H was the first bond in top file.As one who had used gromacs should know that the gromacs top file looked like:
===========================
; Include forcefield parameters
#include "ffG43a1.itp"
#include "s1360.itp"
#include "ions.itp"
[ moleculetype ]
; Name nrexcl
Protein_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 NL 1 CYSH N 1 0.129 14.0067 ; qtot 0.129
2 H 1 CYSH H1 1 0.248 1.008 ; qtot 0.377
3 H 1 CYSH H2 1 0.248 1.008 ; qtot 0.625
..............
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_2
1 3 2 gb_2
======================
This file indicates that the force field of the atoms are included in another files(namely,ffG43a1.itp etc.), and also I had copied these files to local directory.
Does anyone know the reason and any suggestion?
Thank you in advance!
Sting
pair.conf
==============================
gromacs on
grotopfile TEQ2NO.top
coordinates ../avg_wild_TEQ_md.pdb
# initial config
temperature 310
# output params
outputname pairforce
binaryoutput no
# integrator params
timestep 2.0
# force field params
#structure 1wdn_wb.psf
#paraTypeCharmm on
#parameters ../par_all27_prot_lipid.inp
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 13.5
stepspercycle 10
# Atoms in group 1 have a 1 in the B column; group 2 has a 2.
pairInteraction on
pairInteractionFile ref.pdb
pairInteractionCol B
pairInteractionGroup1 1
pairInteractionGroup2 2
# First frame saved was frame 1000.
set ts 0
coorfile open trr ../wild_TEQ_md.trr
# Read all frames until nonzero is returned.
while { ![coorfile read] } {
# Set firstTimestep so our energy output has the correct TS.
firstTimestep $ts
# Compute energies and forces, but don't try to move the atoms.
run 0
incr ts 100
====================
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