From: Mahad Gatti (Mahad.Gatti_at_iit.it)
Date: Thu Sep 22 2016 - 10:07:34 CDT
Hi everyone,
I've been trying to produce CG models using Martini FF to simulate with NAMD, specifically do umbrella sampling simulations. For what I understood so far you can choose to follow the NAMD tutorial or use the CHARMM-GUI website to produce immediately the model.
I tried to do both and in both cases I receive errors regarding parameters. I will focus on the CHARMM-GUI operation now and then move on to the tutorial.
I got the .psf and .pdb, after submitting my .pdb file, and I proceeded to write the input for namd while adding the strings:
cosAngles on
martiniSwitching on
dielectric 15.0
PME off
I used martini2.2 and set up my input like this:
# NAMD Config file - autogenerated by NAMDgui plugin
# Author: Jan Saam, saam_at_charite.de
# input
coordinates step3_pbcsetup.pdb
structure step3_pbcsetup.xplor.psf
paraTypeCharmm on
parameters toppar/martini_v2.2_aminoacids.auto.namd.cons.prm
#parameters toppar/par_all36_prot.prm
#mergeCrossterms yes
#parameters toppar/par_all36_lipid.prm
#parameters toppar/par_all36_carb.prm
#parameters toppar/par_all36_cgenff.prm
#parameters step3_pbcsetup.str
parameters ../toppar_water_ions_namd.str
# output
set output step3_pbcsetup
outputname $output
dcdfile ${output}.dcd
xstFile ${output}.xst
dcdfreq 50
xstFreq 50
binaryoutput no
binaryrestart no
outputEnergies 100
restartfreq 1000
fixedAtoms off
# Basic dynamics
exclude scaled1-4
1-4scaling 1
COMmotion no
#dielectric 1.0
# Simulation space partitioning
switching on
switchdist 9
cutoff 10
pairlistdist 12
# Multiple timestepping
firsttimestep 0
timestep 1
stepspercycle 20
nonbondedFreq 2
fullElectFrequency 4
# Temperature control
set temperature 298
temperature $temperature; # initial temperature
#Martini
cosAngles on
martiniSwitching on
dielectric 15.0
PME off
# Scripting
minimize 1000
reinitvels $temperature
run 10000
And the error is:
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC
I saw, from others questions http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2012-2013/3534.html , that this should be related with the wrong parameters for the TIP3P water model. One of the solutions should be to add the "toppar_water_ions_namd.str" which I did but did not change the outcome. My guess is that there is a problem with the reading of the parameters either because they are the wrong ones either because NAMD cannot read them properly.
If I load all of the par_*.rpm (like explained here: http://mackerell.umaryland.edu/~kenno/cgenff/program.php#namd ) I get:
Reason: FATAL ERROR: BAD ANGLE FORMAT IN CHARMM PARAMETER FILE
LINE=*NH2 CT1 HB1 38.000 109.50 50.00 2.1400 ! From LSN NH2-CT2-HA*
Which is related to a bad understanding of CHARMM syntax?
I hope somebody can help me in finding a solution. All of the toppar files I retrieve them from the folder that CHARMM-GUI gives at the end of the process.
Many thanks in advance and best regards.
Mahad
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