From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
Date: Wed Jun 09 2004 - 04:22:00 CDT
Hello Brian and others,
Brian wrote:
>The first problem is that your psf file does not have a TEST segid that
>your are calling for in your psfgen script.
I did try using the segid in the psffile, MOL, but then I run into the following error:
% segment MOL {readpsf des.psf}
building segment MOL
reading structure from psf file des.psf
Info: generating structure...
unknown residue type MOL
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
Brian wrote:
>Second what is your purpose for reading in this psf file in the first
>place?
The reason I want to read in the psf is because I want to create 1 psf containing my ligand (DES) and the protein (ERalpha), so I can subsequently use the combined psf in the VMD solvate-plugin. By using the already created psf-file of DES, I don't have to create a topology file (I hope).
If anyone could tell me how to read in the psf in a way that subsequently the corresponding pdb-file can be read in, I'd be very pleased.
(If I simply read in the psf for DES, create the psf-info for the protein and then write out the combined psf, I run into the (expected) "no segment
Warning: failed to set coordinate for atom H93 MOL:1 " problem.)
Regards,
Marc
-----Original Message-----
From: Brian Bennion [mailto:brian_at_youkai.llnl.gov]
Sent: Tue 8-6-2004 19:01
To: Kamp, Marc vander
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: psfgen problem
Hi Marc,
The first problem is that your psf file does not have a TEST segid that
your are calling for in your psfgen script.
Second what is your purpose for reading in this psf file in the first
place?
Regards
Brian
On Tue, 8 Jun 2004, Kamp, Marc vander wrote:
> Hi All,
>
> I am trying to read in a psf and pdb file of a DES molecule in psfgen. This should be a simple procedure, however, when I read in the coordinates from the pdb-file after creating the segment with the psf-file, the coordinates can not be set because somehow the residue is not recongnized:
>
> % segment TEST {readpsf des.psf}
> % coordpdb des.pdb TEST
> building segment DES
> reading structure from psf file des.psf
> Info: generating structure...
> Info: segment complete.
> % coordpdb des.pdb TEST
> reading coordinates from pdb file des.pdb for segment TEST
> no residue 1 of segment TEST
> Warning: failed to set coordinate for atom CP9 MOL:1 TEST
> no residue 1 of segment TEST
> Warning: failed to set coordinate for atom CP8 MOL:1 TEST
>
> ... and so on for every atom
>
> The atomnames and residue name and number are identical in my psf and pdb file (see below). The format of both files seems to be OK too (?) and reading in the psf and pdb file in VMD does work. So I don't know what causes the problem.... Can anybody help?
>
> Thanks in advance,
>
> Marc
>
> des.pdb:
> ATOM 1 CP9 MOL 1 5.397 -3.084 -6.170 1.00 0.00
> ATOM 2 CP8 MOL 1 5.818 -2.066 -5.153 1.00 0.00
> ATOM 3 CP7 MOL 1 5.059 -0.745 -5.231 1.00 0.00
> ATOM 4 CP6 MOL 1 3.559 -0.898 -5.064 1.00 0.00
> ATOM 5 CP1 MOL 1 2.972 -0.997 -3.792 1.00 0.00
> ATOM 6 CP2 MOL 1 1.576 -1.171 -3.657 1.00 0.00
> ATOM 7 CP3 MOL 1 0.781 -1.244 -4.800 1.00 0.00
> ATOM 8 OP3 MOL 1 -0.587 -1.444 -4.729 1.00 0.00
> ATOM 9 CP4 MOL 1 1.351 -1.144 -6.071 1.00 0.00
> ATOM 10 CP5 MOL 1 2.729 -0.973 -6.185 1.00 0.00
> ATOM 11 C7 MOL 1 5.633 0.426 -5.443 1.00 0.00
> ATOM 12 C6 MOL 1 7.108 0.549 -5.815 1.00 0.00
> ATOM 13 C5 MOL 1 7.536 0.304 -7.125 1.00 0.00
> ATOM 14 C4 MOL 1 8.886 0.438 -7.482 1.00 0.00
> ATOM 15 C3 MOL 1 9.819 0.817 -6.522 1.00 0.00
> ATOM 16 O3 MOL 1 11.161 0.944 -6.829 1.00 0.00
> ATOM 17 C2 MOL 1 9.422 1.069 -5.204 1.00 0.00
> ATOM 18 C1 MOL 1 8.063 0.928 -4.868 1.00 0.00
> ATOM 19 C8 MOL 1 4.899 1.768 -5.401 1.00 0.00
> ATOM 20 C9 MOL 1 4.970 2.478 -4.072 1.00 0.00
> ATOM 21 HP9 MOL 1 5.952 -4.050 -6.113 1.00 0.00
> ATOM 22 HP9 MOL 1 5.464 -2.657 -7.198 1.00 0.00
> ATOM 23 HP9 MOL 1 4.322 -3.312 -5.980 1.00 0.00
> ATOM 24 HP8 MOL 1 6.917 -1.887 -5.214 1.00 0.00
> ATOM 25 HP8 MOL 1 5.613 -2.503 -4.148 1.00 0.00
> ATOM 26 HP1 MOL 1 3.606 -0.938 -2.891 1.00 0.00
> ATOM 27 HP2 MOL 1 1.119 -1.248 -2.656 1.00 0.00
> ATOM 28 HP3 MOL 1 -1.129 -1.494 -5.508 1.00 0.00
> ATOM 29 HP4 MOL 1 0.718 -1.200 -6.973 1.00 0.00
> ATOM 30 HP5 MOL 1 3.178 -0.895 -7.190 1.00 0.00
> ATOM 31 H5 MOL 1 6.800 0.001 -7.889 1.00 0.00
> ATOM 32 H4 MOL 1 9.206 0.244 -8.519 1.00 0.00
> ATOM 33 H3 MOL 1 11.798 1.203 -6.174 1.00 0.00
> ATOM 34 H2 MOL 1 10.160 1.372 -4.443 1.00 0.00
> ATOM 35 H1 MOL 1 7.743 1.122 -3.830 1.00 0.00
> ATOM 36 H81 MOL 1 3.837 1.640 -5.717 1.00 0.00
> ATOM 37 H82 MOL 1 5.386 2.431 -6.153 1.00 0.00
> ATOM 38 H91 MOL 1 4.435 3.456 -4.041 1.00 0.00
> ATOM 39 H92 MOL 1 6.032 2.606 -3.756 1.00 0.00
> ATOM 40 H93 MOL 1 4.483 1.815 -3.320 1.00 0.00
> TER 41 MOL 1
> CONECT 1 2 21 22 23
> CONECT 2 1 3 24 25
> CONECT 3 2 4 11
> CONECT 4 5 10 3
> CONECT 5 6 4 26
> CONECT 6 5 7 27
> CONECT 7 6 8 9
> CONECT 8 7 28
> CONECT 9 7 10 29
> CONECT 10 9 4 30
> CONECT 11 3 12 19
> CONECT 12 11 13 18
> CONECT 13 12 14 31
> CONECT 14 13 15 32
> CONECT 15 14 16 17
> CONECT 16 15 33
> CONECT 17 15 18 34
> CONECT 18 12 17 35
> CONECT 19 11 20 36 37
> CONECT 20 19 38 39 40
> CONECT 21 1
> CONECT 22 1
> CONECT 23 1
> CONECT 24 2
> CONECT 25 2
> CONECT 26 5
> CONECT 27 6
> CONECT 28 8
> CONECT 29 9
> CONECT 30 10
> CONECT 31 13
> CONECT 32 14
> CONECT 33 16
> CONECT 34 17
> CONECT 35 18
> CONECT 36 19
> CONECT 37 19
> CONECT 38 20
> CONECT 39 20
> CONECT 40 20
> MASTER 3 0 0 0 0 0 0 0 40 1 40 0
> END
>
> des.psf:
> PSF
> 3 !NTITLE
> * File created by pdb2psf.sh
> * (Script from Marc van der Kamp)
> * DATE: Mon Jun 07 15:21:39 CEST 2004
> 40 !NATOM
> 1 MOL 1 MOL CP9 c3 -0.072859 12.0100 0
> 2 MOL 1 MOL CP8 c3 -0.043313 12.0100 0
> 3 MOL 1 MOL CP7 ce -0.041752 12.0100 0
> 4 MOL 1 MOL CP6 ca -0.029927 12.0100 0
> 5 MOL 1 MOL CP1 ca -0.070293 12.0100 0
> 6 MOL 1 MOL CP2 ca -0.051806 12.0100 0
> 7 MOL 1 MOL CP3 ca 0.049209 12.0100 0
> 8 MOL 1 MOL OP3 oh -0.409587 16.0000 0
> 9 MOL 1 MOL CP4 ca -0.051806 12.0100 0
> 10 MOL 1 MOL CP5 ca -0.070293 12.0100 0
> 11 MOL 1 MOL C7 cf -0.041752 12.0100 0
> 12 MOL 1 MOL C6 ca -0.029927 12.0100 0
> 13 MOL 1 MOL C5 ca -0.070293 12.0100 0
> 14 MOL 1 MOL C4 ca -0.051806 12.0100 0
> 15 MOL 1 MOL C3 ca 0.049209 12.0100 0
> 16 MOL 1 MOL O3 oh -0.409587 16.0000 0
> 17 MOL 1 MOL C2 ca -0.051806 12.0100 0
> 18 MOL 1 MOL C1 ca -0.070293 12.0100 0
> 19 MOL 1 MOL C8 c3 -0.043313 12.0100 0
> 20 MOL 1 MOL C9 c3 -0.072859 12.0100 0
> 21 MOL 1 MOL HP9 hc 0.027636 1.0080 0
> 22 MOL 1 MOL H6 hc 0.027636 1.0080 0
> 23 MOL 1 MOL H7 hc 0.027636 1.0080 0
> 24 MOL 1 MOL HP8 hc 0.039555 1.0080 0
> 25 MOL 1 MOL H10 hc 0.039555 1.0080 0
> 26 MOL 1 MOL HP1 ha 0.085236 1.0080 0
> 27 MOL 1 MOL HP2 ha 0.088215 1.0080 0
> 28 MOL 1 MOL HP3 ho 0.283505 1.0080 0
> 29 MOL 1 MOL HP4 ha 0.088215 1.0080 0
> 30 MOL 1 MOL HP5 ha 0.085236 1.0080 0
> 31 MOL 1 MOL H5 ha 0.085236 1.0080 0
> 32 MOL 1 MOL H4 ha 0.088215 1.0080 0
> 33 MOL 1 MOL H3 ho 0.283505 1.0080 0
> 34 MOL 1 MOL H2 ha 0.088215 1.0080 0
> 35 MOL 1 MOL H1 ha 0.085236 1.0080 0
> 36 MOL 1 MOL H81 hc 0.039555 1.0080 0
> 37 MOL 1 MOL H82 hc 0.039555 1.0080 0
> 38 MOL 1 MOL H91 hc 0.027636 1.0080 0
> 39 MOL 1 MOL H92 hc 0.027636 1.0080 0
> 40 MOL 1 MOL H93 hc 0.027636 1.0080 0
> 41 !NBOND: bonds
> 1 2 1 21 1 22 1 23
> 2 3 2 24 2 25 3 4
> 3 11 4 5 4 10 5 6
> 5 26 6 7 6 27 7 8
> 7 9 8 28 9 10 9 29
> 10 30 11 12 11 19 12 13
> 12 18 13 14 13 31 14 15
> 14 32 15 16 15 17 16 33
> 17 18 17 34 18 35 19 20
> 19 36 19 37 20 38 20 39
> 20 40
> 68 !NTHETA: angles
> 2 1 21 2 1 22 2 1 23
> 1 2 3 1 2 24 1 2 25
> 21 1 22 21 1 23 22 1 23
> 3 2 24 3 2 25 2 3 4
> 2 3 11 24 2 25 4 3 11
> 3 4 5 3 4 10 3 11 12
> 3 11 19 5 4 10 4 5 6
> 4 5 26 4 10 9 4 10 30
> 6 5 26 5 6 7 5 6 27
> 7 6 27 6 7 8 6 7 9
> 8 7 9 7 8 28 7 9 10
> 7 9 29 10 9 29 9 10 30
> 12 11 19 11 12 13 11 12 18
> 11 19 20 11 19 36 11 19 37
> 13 12 18 12 13 14 12 13 31
> 12 18 17 12 18 35 14 13 31
> 13 14 15 13 14 32 15 14 32
> 14 15 16 14 15 17 16 15 17
> 15 16 33 15 17 18 15 17 34
> 18 17 34 17 18 35 20 19 36
> 20 19 37 19 20 38 19 20 39
> 19 20 40 36 19 37 38 20 39
> 38 20 40 39 20 40
> 94 !NPHI: dihedrals
> 21 1 2 3 21 1 2 24
> 21 1 2 25 22 1 2 3
> 22 1 2 24 22 1 2 25
> 23 1 2 3 23 1 2 24
> 23 1 2 25 1 2 3 4
> 1 2 3 11 24 2 3 4
> 24 2 3 11 25 2 3 4
> 25 2 3 11 2 3 4 5
> 2 3 4 10 2 3 11 12
> 2 3 11 19 11 3 4 5
> 11 3 4 10 4 3 11 12
> 4 3 11 19 3 4 5 6
> 3 4 5 26 3 4 10 9
> 3 4 10 30 3 11 12 13
> 3 11 12 18 3 11 19 20
> 3 11 19 36 3 11 19 37
> 10 4 5 6 10 4 5 26
> 5 4 10 9 5 4 10 30
> 4 5 6 7 4 5 6 27
> 4 10 9 7 4 10 9 29
> 26 5 6 7 26 5 6 27
> 5 6 7 8 5 6 7 9
> 27 6 7 8 27 6 7 9
> 6 7 8 28 6 7 9 10
> 6 7 9 29 9 7 8 28
> 8 7 9 10 8 7 9 29
> 7 9 10 30 29 9 10 30
> 19 11 12 13 19 11 12 18
> 12 11 19 20 12 11 19 36
> 12 11 19 37 11 12 13 14
> 11 12 13 31 11 12 18 17
> 11 12 18 35 11 19 20 38
> 11 19 20 39 11 19 20 40
> 18 12 13 14 18 12 13 31
> 13 12 18 17 13 12 18 35
> 12 13 14 15 12 13 14 32
> 12 18 17 15 12 18 17 34
> 31 13 14 15 31 13 14 32
> 13 14 15 16 13 14 15 17
> 32 14 15 16 32 14 15 17
> 14 15 16 33 14 15 17 18
> 14 15 17 34 17 15 16 33
> 16 15 17 18 16 15 17 34
> 15 17 18 35 34 17 18 35
> 36 19 20 38 36 19 20 39
> 36 19 20 40 37 19 20 38
> 37 19 20 39 37 19 20 40
> 14 !NIMPHI: impropers
> 3 2 4 11 4 3 5 10
> 11 3 12 19 5 4 6 26
> 10 4 9 30 6 5 7 27
> 7 6 8 9 9 7 10 29
> 12 11 13 18 13 12 14 31
> 18 12 17 35 14 13 15 32
> 15 14 16 17 17 15 18 34
> 2 !NDON: donors
> 8 28 16 33
> 2 !NACC: acceptors
> 8 0 16 0
> 0 !NNB
> 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0
> 1 0 !NGRP NST2
> 0 2 0
>
>
*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************
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