Martini CG models parameters errors

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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