From: Chaya Stern (chaya.stern_at_choderalab.org)
Date: Mon Oct 06 2014 - 16:51:46 CDT

Hi Josh,

I downloaded the latest VMD 1.9.2b1 and it's still not working...

On Mon, Oct 6, 2014 at 5:31 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Hi Chaya,
> What's you VMD version? Carbohydrate atomtypes are often longer than 4
> characters, and in VMD 1.9.1, long atomtypes would also cause psfgen to
> choke (it would truncate them down to 4, which would cause problems). That
> has been fixed in 1.9.2b1 to the best of my knowledge, so if you aren't
> using the latest beta, that is likely the issue.
> -Josh Vermaas
>
> On 10/06/2014 04:25 PM, Chaya Stern wrote:
>
> 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
>>
>>
>>
>
>