VMD-L Mailing List

From: Magnus Andersson (magnus.andersson_at_alumni.chalmers.se)
Date: Wed Apr 05 2017 - 04:48:25 CDT

Hi!

I am getting the following error when running namd:

FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT

This refers to my C-terminal in the protein.

What is strange is that this works fine if I only simulate the protein
(without lipids, water and ions).

My psfgen file looks like:

######################################
package require psfgen

resetpsf

topology toppar_mass_orig/top_all36_prot.rtf
topology toppar_mass_orig/top_all36_lipid.rtf
topology toppar_mass_orig/toppar_water_ions.str

pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD

# add the protein
segment A {
        first NTER
        pdb protein.pdb
        mutate 6 GLY
        mutate 62 GLY
        last CTER
        }
patch GLUP A:32
regenerate angles dihedrals
coordpdb protein.pdb A

# add the lipids
segment POPE {
        pdb POPE.pdb
}
coordpdb POPE.pdb POPE

# add the waters
for {set i 0} {$i < 2} {incr i} {
        segment WAT${i} {
                pdb WAT${i}.pdb
                auto none
        }
coordpdb WAT${i}.pdb WAT${i}
}
for {set i 0} {$i < 2} {incr i} {
        segment WT${i} {
                pdb WT${i}.pdb
                auto none
        }
        coordpdb WT${i}.pdb WT${i}
}

# add the ions
segment ION {
        pdb IONS.pdb
}
coordpdb IONS.pdb ION

guesscoord

writepsf A.psf
writepdb A.pdb

######################################

The output from psfgen is as follows:

psfgen) clearing structure, preserving topology and aliases
psfgen) reading topology file toppar_mass_orig/top_all36_prot.rtf

psfgen) >>>>>>>>CHARMM36 All-Hydrogen Topology File for Proteins <<<<<<

psfgen) >>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<

psfgen) >>>>>>>>>>>>>>>>>>>>>>>>>> May 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<<

psfgen) All comments to the CHARMM web site: www.charmm.org

psfgen) parameter set discussion forum

psfgen)

psfgen) Created by CHARMM version 36 1

psfgen) ERROR! Failed to parse autogenerate statement. Line 92: AUTO
ANGLES DIHE PATCH

psfgen) cross-term entries present in topology definitions

psfgen) reading topology file toppar_mass_orig/top_all36_lipid.rtf

psfgen) \\\\\\\ CHARMM36 All-Hydrogen Lipid Topology File ///////

psfgen) All comments and questions should be submitted to the

psfgen) parameter forum at the CHARMM website: www.charmm.org

psfgen)

psfgen) Created by CHARMM version 36 1

psfgen) ERROR! Failed to parse autogenerate statement. Line 76:
AUTOGENERATE ANGLES DIHEDRALS PATCH

psfgen) reading topology file toppar_mass_orig/toppar_water_ions.str

psfgen) Toplogy and parameter information for water and ions.

psfgen)

psfgen) ERROR! FAILED TO RECOGNIZE SET. Line 35: set nat ?NATC

psfgen) ERROR! FAILED TO RECOGNIZE SET. Line 36: set app

psfgen) ERROR! FAILED TO RECOGNIZE IF. Line 40: if "@NAT" ne "?NATC" if
@nat ne 0 set app append

psfgen) ERROR! FAILED TO RECOGNIZE READ. Line 42: read rtf card @app

psfgen) Topology for water and ions

psfgen)

psfgen) ERROR! FAILED TO RECOGNIZE 31. Line 45: 31 1

psfgen) skipping statements at end of file due to end or return statement

psfgen) aliasing residue HIS to HSE

psfgen) aliasing residue ILE atom CD1 to CD

psfgen) building segment A

psfgen) setting patch for first residue to NTER

psfgen) reading residues from pdb file protein.pdb

psfgen) extracted 407 residues from pdb file

psfgen) mutating residue 6 from ASN to GLY

psfgen) mutating residue 62 from LEU to GLY

psfgen) setting patch for last residue to CTER

psfgen) Info: generating structure...psfgen) Info: skipping improper
N-C-CA-HN at beginning of segment.

psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment--001a1141f14c40c529054c684b2f--