From: Mortimer Hemmit (mortimer.hemmit_at_gmail.com)
Date: Fri Feb 28 2020 - 18:42:37 CST
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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