VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Apr 05 2017 - 05:15:38 CDT

2 things here:

1) The Psfgen out is showing errors. Does the output file A.psf and A.pdb
get written ? Do they look ok? You should comment out the lines in the
topology files which are generating the error and ensure you have proper
A.psf and A.pdb produced using the topology you want to use.

2) Did you run the simulation using the same verison 36?? The type of error
you are showing appears when the versions are mixed up i.e. the pdb and psf
have atomtypes from possibly CHARMM27 and you are trying to run it using
CHARMM36.

Not sure if this will help - but you should definitely look up these two
points.

Hope this helps.

Best,
/A

On Wed, Apr 5, 2017 at 9:48 PM, Magnus Andersson <
magnus.andersson_at_alumni.chalmers.se> wrote:

> 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 

-- 
Best,
/A