VMD-L Mailing List

From: Takeru KAMEDA (kamedapon_at_hiroshima-u.ac.jp)
Date: Tue May 28 2019 - 08:28:06 CDT

Dear Peter

Thank you for your advising.

We tried following command :

=========================================================
resetpsf

autopsf -protein -nucleic -prefix psfgen -top ./../toppar/top_all36_na.rtf -top ./../toppar/top_all36_prot.rtf -top ./../toppar/top_all36_carb.rtf -top ./../toppar/top_all36_lipid.rtf
=========================================================

and GUI interface.
However, following error was print :

=========================================================
segfiles psfgen_formatted_autopsf-temp.pdb_AP1.pdb psfgen_formatted_autopsf-temp.pdb_BP1.pdb psfgen_formatted_autopsf-temp.pdb_CP1.pdb psfgen_formatted_autopsf-temp.pdb_DP1.pdb psfgen_formatted_autopsf-temp.pdb_EP1.pdb psfgen_formatted_autopsf-temp.pdb_FP1.pdb psfgen_formatted_autopsf-temp.pdb_GP1.pdb psfgen_formatted_autopsf-temp.pdb_HP1.pdb psfgen_formatted_autopsf-temp.pdb_IP1.pdb psfgen_formatted_autopsf-temp.pdb_IP2.pdb psfgen_formatted_autopsf-temp.pdb_JP1.pdb psfgen_formatted_autopsf-temp.pdb_KP1.pdb psfgen_formatted_autopsf-temp.pdb_LP1.pdb psfgen_formatted_autopsf-temp.pdb_MP1.pdb psfgen_formatted_autopsf-temp.pdb_MP2.pdb psfgen_formatted_autopsf-temp.pdb_NP1.pdb psfgen_formatted_autopsf-temp.pdb_OP1.pdb psfgen_formatted_autopsf-temp.pdb_PP1.pdb psfgen_formatted_autopsf-temp.pdb_QP1.pdb psfgen_formatted_autopsf-temp.pdb_RP1.pdb psfgen_formatted_autopsf-temp.pdb_RP2.pdb psfgen_formatted_autopsf-temp.pdb_SP1.pdb psfgen_formatted_autopsf-temp.pdb_TP1.pdb psfgen_formatted_autopsf-temp.pdb_UP1.pdb psfgen
_formatted_autopsf-temp.pdb_VP1.pdb psfgen_formatted_autopsf-temp.pdb_WP1.pdb psfgen_formatted_autopsf-temp.pdb_XP1.pdb psfgen_formatted_autopsf-temp.pdb_YP1.pdb psfgen_formatted_autopsf-temp.pdb_ZP1.pdb psfgen_formatted_autopsf-temp.pdb_aP1.pdb psfgen_formatted_autopsf-temp.pdb_bP1.pdb psfgen_formatted_autopsf-temp.pdb_cP1.pdb psfgen_formatted_autopsf-temp.pdb_dP1.pdb psfgen_formatted_autopsf-temp.pdb_eP1.pdb psfgen_formatted_autopsf-temp.pdb_fP1.pdb psfgen_formatted_autopsf-temp.pdb_gP1.pdb psfgen_formatted_autopsf-temp.pdb_gP2.pdb psfgen_formatted_autopsf-temp.pdb_gP3.pdb psfgen_formatted_autopsf-temp.pdb_hP1.pdb psfgen_formatted_autopsf-temp.pdb_iP1.pdb psfgen_formatted_autopsf-temp.pdb_jP1.pdb psfgen_formatted_autopsf-temp.pdb_jP2.pdb psfgen_formatted_autopsf-temp.pdb_jP3.pdb psfgen_formatted_autopsf-temp.pdb_kP1.pdb psfgen_formatted_autopsf-temp.pdb_kP2.pdb psfgen_formatted_autopsf-temp.pdb_kP3.pdb psfgen_formatted_autopsf-temp.pdb_kP4.pdb psfgen_formatted_autopsf-temp.pdb_kP5.pdb psfgen_formatt!
 ed_autop
sf-temp.pdb_kP6.pdb psfgen_formatted_autopsf-temp.pdb_kP7.pdb psfgen_formatted_autopsf-temp.pdb_kP8.pdb psfgen_formatted_autopsf-temp.pdb_lP1.pdb psfgen_formatted_autopsf-temp.pdb_mP1.pdb psfgen_formatted_autopsf-temp.pdb_1N1.pdb psfgen_formatted_autopsf-temp.pdb_2N1.pdb psfgen_formatted_autopsf-temp.pdb_2N2.pdb psfgen_formatted_autopsf-temp.pdb_3N1.pdb
psfgen_formatted_autopsf-temp.pdb_AP1.pdb
1 1625
psfgen) building segment AP1
psfgen) reading residues from pdb file psfgen_formatted_autopsf-temp.pdb_AP1.pdb
psfgen) extracted 97 residues from pdb file
psfgen) setting patch for first residue to NTER
psfgen) setting patch for last residue to CTER
psfgen) Info: generating structure...psfgen) unknown patch type CTER
failed!
Info) Coordinate I/O rate 0.19 frames/sec, 0 MB/sec, 5.2 sec
Info) Finished with coordinate file psfgen_formatted.pdb.
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
=========================================================

Why such error was shown?

Any editing of PDB file are necessary ?

Thank you in advance.
Best wishes,
Takeru Kameda
PhD Student, Hiroshima University, Japan

________________________________________
$B:9=P?M(B: Peter Freddolino <petefred_at_umich.edu>
$BAw?.F|;~(B: 2019$BG/(B5$B7n(B27$BF|(B 22:47
$B08_at_h(B: Takeru KAMEDA
CC: vmd-l_at_ks.uiuc.edu
$B7oL>(B: Re: psfgen problems of many segment complex

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<mailto: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/3j8145616433999940&sdata=R6X%2BZ4oNjCR5HH%2BebBb7GvLmhiac225ayiRvTrXXO84%3D&reserved=0>)
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.shtml0d3750%7C1%7C0%7C636945616434009934&sdata=wFXSZtV0nhA%2F%2FWuvUJviNV%2B0gXwWKuZtTY5JwD3%2FHR4%3D&reserved=0>)
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
""""""""""""""""""""""""""""""""""""""""""""""""" 

--
________________________________
$B:9=P?M(B: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>>
$BAw?.F|;~(B: 2019$BG/(B5$B7n(B24$BF|(B 21:52
$B08_at_h(B: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>; Takeru KAMEDA
$B7oL>(B: 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<mailto: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