From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Dec 10 2015 - 15:30:14 CST
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
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