VMD-L Mailing List

From: Chaya Stern (chaya.stern_at_choderalab.org)
Date: Mon Oct 06 2014 - 16:25:30 CDT

Hi Josh,

I tried doing that with the toppar_all36_lipid_cholesterol.str and
toppar_all36_lipid_detergent.str. It worked for the cholesterol but not
detergent. After trying each residue separately in the detergent stream
file I found that psfgen only runs into this problem when there are both
carb and lipid atom types. However, adding top_all36_carp.rtf doesn't solve
the problem. So I really don't know what else to try.

On Mon, Oct 6, 2014 at 5:09 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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
> 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
>
>
>