Re: bad angle error!!

From: ROPÓN-PALACIOS G. (biodano.geo_at_gmail.com)
Date: Fri Feb 28 2020 - 14:51:44 CST

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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