VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Oct 06 2014 - 16:09:00 CDT

Hi Chaya,

psfgen and stream files never liked one another very much, usually since
there are CHARMM commands (set, read, if statements, etc.) in stream
files that psfgen doesn't understand (psfgen expects topology files, not
mixed ones). What I do is strip those commands out and make a new "pure"
topology file that lacks these commands and the parameters. I'm super
suspicious as to what selective stream files worked fine, because this
is what a session with an unadulterated toppar file looks like using the
most recent beta:

psfgen) reading topology file toppar_all36_lipid_cholesterol.str

psfgen) Toppar stream file for cholesterol. Stream following reading of
psfgen) top_all36_lipid.rtf
psfgen) par_all36_lipid.rtf
psfgen) top_all36_cgenff.rtf
psfgen) and par_all36_cgenff.prm
psfgen)
psfgen) ERROR! FAILED TO RECOGNIZE SET
psfgen) ERROR! FAILED TO RECOGNIZE SET
psfgen) ERROR! FAILED TO RECOGNIZE IF
psfgen) ERROR! FAILED TO RECOGNIZE READ
psfgen) Topology for cholesterol
psfgen)
psfgen) ERROR! FAILED TO RECOGNIZE 31
psfgen) skipping statements at end of file due to end or return statement

-Josh

On 10/06/2014 03:01 PM, Chaya Stern wrote:
> Hello,
>
> 'm having trouble with psfgen parsing the
> toppar_all36_lipid_detergent.str file that I downloaded from
> MacKerrel's lab page. I've made no changes to the file and this is
> what I get when psf tries to parse it
>
> psfgen) reading topology file ../topology/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
> <http://www.charmm.org>
> psfgen)
> psfgen) Created by CHARMM version 36 1
> psfgen) reading topology file ../topology/toppar_all36_lipid_detergent.str
>
> psfgen) Toppar stream file for detergents. Stream following reading of
> psfgen) top_all36_lipid.rtf
> psfgen) and
> psfgen) par_all36_lipid.rtf
> psfgen)
> psfgen) reading topology from stream file
> psfgen) detergent residues
> psfgen)
> psfgen) Created by CHARMM version 36 1
> psfgen) ERROR! Failed to parse atom statement.
> psfgen) ERROR! Failed to parse atom statement.
> psfgen) ERROR! Failed to parse atom statement.
> psfgen) ERROR! Failed to parse atom statement.
> psfgen) ERROR! Failed to parse atom statement.
> psfgen) ERROR! Failed to parse atom statement.
> psfgen) ERROR! Failed to parse atom statement.
> psfgen) ERROR! Failed to parse atom statement.
> psfgen) ERROR! Failed to parse atom statement.
> psfgen) ERROR! Failed to parse atom statement.
> psfgen) ERROR! Failed to parse atom statement.
> psfgen) ERROR! Failed to parse atom statement.
>
> So then I tried adding the top_all36_carb and top_all36_prot to get
> all the atom types but the problem persisted. I also tried parsing
> other stream files in the stream directory and there was no problem
> there. I didn't find any weird special characters either in the file.
>
> Thanks,
> Chaya