Re: vmd-l: PRES and water-ions issues with charmm36

From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Thu Dec 10 2015 - 15:58:49 CST

I believe you meant to use the "patch" command instead of "pres" (which
doesn't exist in psfgen). In general, you should use "regenerate angles
dihedrals" /after/ you apply a patch (otherwise only the 1-2 bonded term
gets added),

HTH,
Brian

On 12/10/2015 03:30 PM, Francesco Pietra wrote:
> Hello:
> With charmm36, using vmd in text mode "vmd -dispdev ...gen" which is
> organized in eight sectionsas follows:
>
> !st SECTION
> package require psfgen
> topology top_all36_prot.rtf
> topology myion.rtf
> topology toppar_water_ions.str
> topology toppar_all36_prot_heme_O2-mod.str ! mod by zeroing charges
> for O2
> topology tip4p.top ! Freddolino kit
>
> 2nd SECTION
> pdbalias atom ALA H HN
> etc
>
> 3rd SECTION
> segment PRA {
> last CTER
> pdb parts/PROT_A_segnPRA.pdb
> }
> etc
>
> 4th SECTION
> regenerate angles dihedrals
>
> 4th SECTION
> coordpdb parts/PROT_A_segnPRA.pdb PRA
> etc
>
> 6th SECTION
> guesscoord ! although I furnish a protonated protein
>
> 7th SECTION
> PRES DISU PRA:4 PRA:12
> etc
>
> 8th SECTION
> writepsf
> etc
>
>
> I gpt two errors
>
> psfgen) Toplogy and parameter information for water and ions.
> 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 water and ions
> psfgen)
> psfgen) ERROR! FAILED TO RECOGNIZE 31
> psfgen) skipping statements at end of file due to end or return
> statement
>
>
> and
>
> invalid command name "PRES"
>
>
> I read on the forum how to correct autopsf for the first error. Could
> you please indicate how to do for vmd in text mode (I have so many
> components that using autopsf is troublesome). In partcular, is
> "regenerate angles dihedrals" correctly positioned?
>
> thanks
>
> francesco pietra
>

-- 
Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
email: radak_at_uchicago.edu

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:38 CST