From: ROPÓN-PALACIOS G. (biodano.geo_at_gmail.com)
Date: Fri Feb 28 2020 - 18:06:54 CST
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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