VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon May 27 2019 - 08:47:37 CDT

You do not need to give segment names that are the same as the chain names
in the pdb -- in fact I would advise against it. Autopsf, for example, just
calls protein chains P1, P2, etc.

Best,
Peter

On Fri, May 24, 2019 at 11:14 AM Takeru KAMEDA <kamedapon_at_hiroshima-u.ac.jp>
wrote:

> Dear VMD Users
>
> Somehow my previous mail was not sent to the end (Sorry).
> I have a question about how to apply psfgen to a complex with many
> segments.
> We tried to use the structure (PDB: 3J81) with many segments (chains) as
> follows.
> A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k
> l m 1 2 3
> (https://www.rcsb.org/structure/3j81)
> However, we could not finish the psfgen script.
> It seems that chain ID is case insensitive and hence e.g. chains A and a
> are regarded as duplicated chain IDs.
> Could you tell me how to solve the problem?
> We employed VMD 1.9.3 (psfgen version1.6.4), and CHARMM36 parameter. (
> http://mackerell.umaryland.edu/charmm_ff.shtml)
> Thank you in advance.
> Best wishes,
>
> Takeru Kameda
> PhD Student, Hiroshima University, Japan
> The PSFgen script we used is as follows:
>
>
> """""""""""""""""""""""""""""""""""""""""""""""""
> package require psfgen
> resetpsf
> topology ./../toppar/top_all36_na.rtf
> topology ./../toppar/top_all36_prot.rtf
> topology ./../toppar/top_all36_carb.rtf
> topology ./../toppar/top_all36_cgenff.rtf
> topology ./../toppar/top_all36_lipid.rtf
> pdbalias residue A ADE
> pdbalias residue G GUA
> pdbalias residue C CYT
> pdbalias residue T THY
> pdbalias residue U URA
> pdbalias residue HIS HSE
> pdbalias atom ILE CD1 CD
> ## protein
> 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"
> set seg ${chain}PRO
> set sel [atomselect top "protein and chain $chain"]
> $sel set segid $seg
> $sel writepdb tmp.pdb
> segment $seg {
> #first NTER
> #last CTER
> pdb tmp.pdb
> }
> coordpdb tmp.pdb
> }
> ## RNA
> set sel [atomselect top nucleic]
> set chains [lsort -unique [$sel get chain]];# return A B C D
> foreach chain $chains {
> puts "Adding RNA chain $chain to psfgen"
> set seg ${chain}RNA
> set sel [atomselect top "nucleic and chain $chain"]
> $sel set segid $seg
> $sel writepdb tmp.pdb
>
> segment $seg { pdb tmp.pdb }
>
> set resids [lsort -unique [$sel get resid]]
> #foreach r $resids {
> #patch DEOX $seg:$r
> #}
> regenerate angles dihedrals
> coordpdb tmp.pdb
> }
> guesscoord
> writepsf psfgen.psf
> writepdb psfgen.pdb
> """""""""""""""""""""""""""""""""""""""""""""""""
> --
>
> ------------------------------
> *差出人:* Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> *送信日時:* 2019年5月24日 21:52
> *宛先:* vmd-l_at_ks.uiuc.edu; Takeru KAMEDA
> *件名:* RE: psfgen problems of many segment complex
>
> One segment at a time would be my advice. That's how the psfgen user guide
> does it (see page 4, where the protein BPTI is in a different segment than
> the water).
>
> -Josh
>
>
>
> On 2019-05-24 00:56:17-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Dear VMD Users
>
> I have a question about how to apply psfgen to a complex with many segments
>
>