Re: bad angle error!!

From: ROPÓN-PALACIOS G. (biodano.geo_at_gmail.com)
Date: Fri Feb 28 2020 - 19:40:22 CST

yes my problem is when correctthis O --> OT1 and have following problem:

warning failed guess gue bad angle OT1 C OT2

El vie., 28 de feb. de 2020 a la(s) 19:42, Mortimer Hemmit (
mortimer.hemmit_at_gmail.com) escribió:

> PDB documentation uses O and OXT, but psfgen prefers OT1 and OT2 instead.
>
>
> On Fri, Feb 28, 2020 at 7:37 PM ROPÓN-PALACIOS G. <biodano.geo_at_gmail.com>
> wrote:
> >
> > change of O to OT1 is for warning problem for set coordinates correctly
> >
> >
> > El vie., 28 de feb. de 2020 a la(s) 17:44, Josh Vermaas (
> joshua.vermaas_at_gmail.com) escribió:
> >>
> >> Ok, this is confusing to me. I tried out your script, uncommenting the
> regenerate angles dihedrals stuff (you can't skip it!), and I got something
> that looked reasonable when I started from the pdb structure. Why are you
> changing the atom names? The O atoms are usually the carbonyl oxygens in
> the protein backbone, and renaming them is probably going to be bad. The
> script I settled on was below.
> >>
> >> -Josh
> >>
> >> package require psfgen
> >> topology top_all36_prot.rtf
> >> topology top_all36_na.rtf
> >>
> >>
> >> ;## BUNDLE 1 OF RIBOSOME
> >> mol new 6spb.pdb type pdb waitfor all
> >>
> >> ;# protein get chains
> >> set sel [atomselect top "protein"]
> >> set chains [lsort -unique [$sel get chain]] ;# return A B C D
> >> foreach chain $chains {
> >> puts "Adding protein chain $chain to psfgen"
> >> pdbalias residue HIS HSD
> >> pdbalias atom ILE CD1 CD
> >> set seg ${chain}PRO
> >> set sel [atomselect top "protein and chain $chain"]
> >> $sel set segid $seg
> >> $sel writepdb tmp.pdb
> >> segment $seg { pdb tmp.pdb
> >> first NTER
> >> last CTER
> >> }
> >> regenerate angles dihedrals ; # critical after patching
> >> coordpdb tmp.pdb
> >> }
> >> guesscoord
> >>
> >> ;# DNA get chains
> >> mol delete all
> >> mol delete $sel
> >> mol new 6spb.pdb type pdb waitfor all
> >> set sel [atomselect top "nucleic"]
> >> set chains [lsort -unique [$sel get chain]] ;# return A B C D
> >> foreach chain $chains {
> >> puts "Adding DNA chain $chain to psfgen"
> >> ;# Nucleic acid pdbalias
> >> pdbalias residue A ADE
> >> pdbalias residue G GUA
> >> pdbalias residue C CYT
> >> ;#pdbalias residue T THY ;# Only for DNA
> >> pdbalias residue U URA ;# Only for RNA
> >> pdbalias atom A OP1 O1P
> >> pdbalias atom A OP2 O2P
> >> pdbalias atom G OP1 O1P
> >> pdbalias atom G OP2 O2P
> >> pdbalias atom C OP1 O1P
> >> pdbalias atom C OP2 O2P
> >> pdbalias atom U OP1 O1P
> >> pdbalias atom U OP2 O2P
> >> set seg ${chain}RNA
> >> set sel [atomselect top "nucleic and chain $chain"]
> >> $sel set segid $seg
> >> $sel writepdb tmp.pdb
> >>
> >> segment $seg { pdb tmp.pdb }
> >> #only for DNA
> >> #set resids [lsort -unique [$sel get resid]]
> >> #foreach r $resids {
> >> # patch DEOX $seg:$r
> >> #}
> >> regenerate angles dihedrals
> >> coordpdb tmp.pdb
> >> }
> >> guesscoord
> >>
> >> ;## Escribiendo los output
> >> writepsf ribosome_top.psf ; # Output PSF
> >> writepdb ribosome_top.pdb ; # Output PDB
> >> quit
> >>
> >>
> >>
> >> On Fri, Feb 28, 2020 at 3:51 PM ROPÓN-PALACIOS G. <
> biodano.geo_at_gmail.com> wrote:
> >>>
> >>> i'm using v1.9.4 last version.
> >>>
> >>> i'm try prepare ribosome topology this is mi code:
> >>> manually i'm change name atom O --> OT1
> >>>
> >>> ############################################
> >>> if {1} {
> >>> package require psfgen
> >>> ;#topology toppar/top_all22_prot.rtf
> >>> topology toppar/top_all36_prot.rtf
> >>> topology toppar/top_all36_na_nbfix.rtf
> >>> ;#topology toppar/top_all36_carb.rtf
> >>> topology toppar/toppar_water_ions_nbfix.str
> >>> }
> >>>
> >>> ;## BUNDLE 1 OF RIBOSOME
> >>> mol new 6SPB.pdb type pdb waitfor all
> >>>
> >>> ;# protein get chains
> >>> set sel [atomselect top "protein"]
> >>> set chains [lsort -unique [$sel get chain]] ;# return A B C D
> >>> foreach chain $chains {
> >>> puts "Adding protein chain $chain to psfgen"
> >>> pdbalias residue HIS HSD
> >>> pdbalias atom ILE CD1 CD
> >>> set seg ${chain}PRO
> >>> set sel [atomselect top "protein and chain $chain"]
> >>> $sel set segid $seg
> >>> #pdbalias atom VAL O OT1
> >>> #pdbalias atom LYS O OT1
> >>> #pdbalias atom ARG O OT1
> >>> #pdbalias atom GLY O OT1
> >>> #pdbalias atom LYS O OT1
> >>> #pdbalias atom ALA O OT1
> >>> #pdbalias atom PRO O OT1
> >>> #pdbalias atom LEU O OT1
> >>> #pdbalias atom GLU O OT1
> >>> #pdbalias atom ASP O OT1
> >>> #pdbalias atom THR O OT1
> >>> #pdbalias atom PHE O OT1
> >>> #pdbalias atom GLN O OT1
> >>> $sel writepdb tmp.pdb
> >>> segment $seg { pdb tmp.pdb
> >>> #first NTER
> >>> #last CTER
> >>> }
> >>> #regenerate angles
> >>> #regenerate resids
> >>> #regenerate angles dihedrals ; # critical after patching
> >>> coordpdb tmp.pdb
> >>> }
> >>> #guesscoord
> >>>
> >>> ;# DNA get chains
> >>> mol delete all
> >>> mol delete $sel
> >>> exec rm tmp.pdb
> >>> mol new 6SPB.pdb type pdb waitfor all
> >>> set sel [atomselect top "nucleic"]
> >>> set chains [lsort -unique [$sel get chain]] ;# return A B C D
> >>> foreach chain $chains {
> >>> puts "Adding DNA chain $chain to psfgen"
> >>> ;# Nucleic acid pdbalias
> >>> pdbalias residue A ADE
> >>> pdbalias residue G GUA
> >>> pdbalias residue C CYT
> >>> ;#pdbalias residue T THY ;# Only for DNA
> >>> pdbalias residue U URA ;# Only for RNA
> >>> pdbalias atom A OP1 O1P
> >>> pdbalias atom A OP2 O2P
> >>> pdbalias atom G OP1 O1P
> >>> pdbalias atom G OP2 O2P
> >>> pdbalias atom C OP1 O1P
> >>> pdbalias atom C OP2 O2P
> >>> pdbalias atom U OP1 O1P
> >>> pdbalias atom U OP2 O2P
> >>> set seg ${chain}RNA
> >>> set sel [atomselect top "nucleic and chain $chain"]
> >>> $sel set segid $seg
> >>> $sel writepdb tmp.pdb
> >>>
> >>> segment $seg { pdb tmp.pdb }
> >>> #only for DNA
> >>> #set resids [lsort -unique [$sel get resid]]
> >>> #foreach r $resids {
> >>> # patch DEOX $seg:$r
> >>> #}
> >>> #regenerate angles dihedrals
> >>> coordpdb tmp.pdb
> >>> }
> >>> guesscoord
> >>>
> >>> ;## Escribiendo los output
> >>> writepsf ribosome_top.psf ; # Output PSF
> >>> writepdb ribosome_top.pdb ; # Output PDB
> >>> quit
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> El vie., 28 de feb. de 2020 a la(s) 08:53, Josh Vermaas (
> joshua.vermaas_at_gmail.com) escribió:
> >>>>
> >>>> What were the steps/script you used to get to this error. Guessing
> coordinates makes me think that this is in the psf generation process, but
> without knowing what you did, its difficult to diagnose the issue.
> >>>>
> >>>> -Josh
> >>>>
> >>>> On 2/27/20 10:10 PM, ROPÓN-PALACIOS G. wrote:
> >>>>
> >>>> Dear namd Users,
> >>>>
> >>>> I have following problem, please help me :
> >>>>
> >>>> #############################################
> >>>> failed to guess coordinate due to bad angle OT1 C OT2
> >>>> ##############################################
> >>>>
> >>>> How can fix this problem?
> >>>>
> >>>> att:
> >>>>
> >>>> geo.
> >>>>
> >>>> --
> >>>>
> >>>
> >>>
> >>> --
> >>>
> >
> >
> > --
> >
>

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