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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