VMD-L Mailing List

From: Chaya Stern (chaya.stern_at_choderalab.org)
Date: Mon Oct 06 2014 - 15:01:48 CDT

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
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