From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Wed Sep 24 2008 - 23:11:04 CDT

yes...i tried that but when i with that pdb& psf file i am trying to solvate the molecule with command:
(ao) 1 % package require solvate
1.2
>Main< (ao) 2 % solvate aoq.psf aoq.pdb -t 10 -o aoq_wb

 
its giving error:
reading structure from psf file aoq.psf
error reading atoms

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>Main< (ao) 3 %

ofcourse the atom with -1 occupency has removed here.
so what should i do to solvate the molecule?

-- 
Rudra
JRF; SNBNCBS
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----- Original Message ----
From: Peter Freddolino <petefred_at_ks.uiuc.edu>
To: Rudra Banerjee <bnrj.rudra_at_yahoo.com>
Cc: vmd-l_at_ks.uiuc.edu
Sent: Thursday, 25 September, 2008 9:31:48 AM
Subject: Re: vmd-l: psf file generation: once again
The solution was suggested by Christopher Chang yesterday: turn off 
automatic patching.
segment U {
pdb blah.pdb
first none
last none
}
(or, don't just insert your residue into the charmm22 files, which have 
default patches defined).
Peter
Rudra Banerjee wrote:
> dear friends,
> I want to repeat one of my unsolved problem. i have a non std. molecule with initial (before generating psf) pdb file is:
>
>
>  #CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
> ATOM      1  CD1  MAC A  1      -3.039   1.934  -0.283  1.00  0.00           C
> ATOM      2  CG   MAC A  1      -3.189   0.892   0.625  1.00  0.00           C
> ATOM      3  CD2  MAC A  1      -2.112   0.042   0.894  1.00  0.00           C
> ATOM      4  CE2  MAC A  1      -0.879   0.204   0.276  1.00  0.00           C
> ATOM      5  CZ   MAC A  1      -0.733   1.261  -0.643  1.00  0.00           C
> ATOM      6  CE1  MAC A  1      -1.812   2.120  -0.917  1.00  0.00           C
> ATOM      8  C3   MAC A  1       1.315  -0..482  -0.029  1.00  0.00           C
> ATOM      9  C2   MAC A  1       1.562   0.544  -0.962  1..00  0.00           C
> ATOM     10  C1   MAC A  1       0.512   1.419  -1.262  1.00  0.00           C
> ATOM     11  C7   MAC A  1       2.353  -1.354   0.273  1.00  0.00           C
> ATOM     12  C6   MAC A  1       3.613  -1.234  -0.321  1.00  0.00           C
> ATOM     13  C5   MAC A  1       3.854  -0.212  -1.232  1.00  0.00           C
> ATOM     14  C4   MAC A  1       2.827   0.670  -1.563  1.00  0.00           C
> ATOM     24  C8   MAC A  1       5.628  -2.116  -0.419  1.00  0.00           C
> ATOM     25  CA   MAC A  1      -5.107   1.352   1.005  1.00  0.00           C
> ATOM     26  CB   MAC A  1      -4.392  -0.073   1.897  1.00  0..00           C
> ATOM     36  C9   MAC A  1       4.407  -3.273   0.925  1..00  0.00           C
> ATOM      7  N    MAC A  1       0.123  -0.642   0..571  1.00  0.00           N
> ATOM     15  N1   MAC A  1       4.671  -2..189   0.006  1.00  0.00           N
> ATOM     16  N2   MAC A  1      -4..299   0.713   1.207  1.00  0.00           N
> ATOM     17  HD1  MAC A  1      -3.879   2.612  -0.492  1.00  0.00           H
> ATOM     18  HD2  MAC A  1      -2.248  -0.784   1.607  1.00  0.00           H
> ATOM     19  HE1  MAC A  1      -1.685   2.949  -1.629  1.00  0.00           H
> ATOM     20  H1   MAC A  1       0.669   2.239  -1.978  1.00  0.00           H
> ATOM     21  H7   MAC A  1       2.175  -2.167   0.992  1.00  0.00           H
> ATOM     22  H5   MAC A  1       4.846  -0.106  -1.696  1.00  0.00           H
> ATOM     23  H4   MAC A  1       3.013   1.474  -2.290  1.00  0.00           H
> ATOM     27  H81  MAC A  1       6.081  -1.136  -0.148  1.00  0.00           H
> ATOM     28  H82  MAC A  1       5.550  -2.185  -1.527  1.00  0.00           H
> ATOM     29  H83  MAC A  1       6.270  -2.939  -0.032  1.00  0.00           H
> ATOM     30  HA2  MAC A  1      -4.830   2.397   1.270  1.00  0.00           H
> ATOM     31  HA1  MAC A  1      -5.986   1..045   1.614  1.00  0.00           H
> ATOM     32  HA3  MAC A  1      -5.354   1.307  -0.080  1.00  0.00           H
> ATOM     33  HB2  MAC A  1      -5.425  -0.085   2.310  1.00  0.00           H
> ATOM     34  HB3  MAC A  1      -4.187  -1.041   1.386  1.00  0.00           H
> ATOM     35  HB1  MAC A  1      -3.663   0.071   2.725  1.00  0.00           H
> ATOM     37  H93  MAC A  1       3.586  -3.909   0.524  1.00  0.00           H
> ATOM     38  H92  MAC A  1       5.323  -3.895   1.040  1.00  0.00           H
> ATOM     39  H91  MAC A  1       4.096  -2.858   1.910  1.00  0.00           H
> END
>
> and for this  molecule, i have generated my topology file(inserted to charmm22 protein topology file)is:
> !MY RESIDUE
>
> RESI MAC      0.00 
> GROUP  
> ATOM N2   NH2     -0.47     !
> ATOM HA1   HB      0.31    !
> ATOM CA    CA      0.07   !
> ATOM HA2   HB      0.09    !
> ATOM HA3   HB       0.00     !
> GROUP                            ! 
> ATOM CB   CA     -0.18       ! 
> ATOM HB1  HB        0.09   !
> ATOM HB2  HB      0...09     !
> ATOM HB3  HB      0.00      !
> GROUP                              !
> ATOM CD1  CA     -0.115    !
> ATOM HD1  HP      0.115    !
> GROUP                              !
> ATOM CE1  CA     -0.115    !    
> ATOM HE1  HP      0.115    !                      HE1   H1   H4
> GROUP                             !                         |       |    |
> ATOM  CZ   CA       0.00      !       HA2   HD1 CE1   C1       C4  H5 H83
> GROUP                             !           |         \ //    \  /   \\   /  \\ /      |
> ATOM  CG  CA       0.00      !  HA1-CA    CD1    CZ   C2    C5  --C8-H82
> GROUP                             !           |       |         ||       |       |       \
> ATOM CD2  CA     -0.115    !   HA3 N2--  CG     CE2    C3    C6-N1  H81
> ATOM HD2  HP      0.115    !          |        \\       /   \     // \   //      |
> GROUP                             !  HB1-CB-HB3 CD2      N      C7     C9-H93
> ATOM CE2  CA      0.47     !          |           |                 /       /  \
> ATOM  N      NR3      -0.47 !         HB2      HD2            H7   H91 H92
> GROUP                             ! 
> ATOM  C1   CA      -0.115   !
> ATOM  H1   HP      0.115     !
> GROUP                             !
> ATOM  C2   CA       0.00       !
> ATOM  C3   CA       0.00       !
> GROUP                             !
> ATOM  C4   CA      -0.115   !
> ATOM  H4   HP      0.115     !
> GROUP                             !
> ATOM  C5   CA      -0.115    !
> ATOM  H5   HP      0.115     !
> GROUP                             !
> ATOM  C7   CA      -0.115   !
> ATOM  H7   HP      0.115     !
> GROUP                             !
> ATOM  C6   CA        0.07    !
> ATOM  N1   NH2    -0.047    !
> ATOM  C8   CA        0.08     !
> ATOM  C9   CA        0.08     !
> ATOM  H81  HB        0.04    !
> ATOM  H82  HB        0.04    !
> ATOM  H83  HB        0.04    !
> ATOM  H91  HB        0.04   !
> ATOM  H92  HB        0.04   !
> ATOM  H93  HB        0.04   !
> BOND  CG CD1 CE1 CZ CZ C1 C2 C3 CE2 CD2 CE2 N C2 C4 C5 C6 N2 CG N1 C6
> BOND  N2 CA CA HA1 CA HA2 CA HA3 N2 CB CB HB1 CB HB2 CB HB3
> BOND  CD1 HD1 CE1 HE1 C1 H1 C4 H4 C5 H5 C7 H7 CD2 HD2 C7 C3
> BOND  N1 C8 N1 C9 C9 H91 C9 H92 C9 H93 C8 H81 C8 H82 C8 H83
> DOUBLE CD1 CE1 CG CD2 CZ CE2 C1 C2 C3 N C4 C5 C6 C7
>
>
> but when i am trying to generate psf file using vmd using the .pgn file (cku.pgn)
>
> package require psfgen
> topology my-top.inp
> #pdbalias residue HIS HSE
> #pdbalias atom ILE CD1 CD
> segment U {pdb ao_tst.pdb} 
> coordpdb ao_tst.pdb U
> guesscoord
> writepdb aoq.pdb
> writepsf aoq.psf
>
> using the command:
> $vmd -dispdev text -e cku.pgn
>
> then i am getting a few extra atom(6 actually) in (0 0 0) position with occupency -1. here is that (part of) generated pdb file:
>
> REMARK original generated coordinate pdb file
> ATOM      1  C   MAC     0       0.000   0.000   0.000 -1.00  0.00      U    C
> ATOM      2  OT1 MAC     0       0.000   0.000   0.000 -1.00  0.00      U    O
> ATOM      3  OT2 MAC     0       0.000   0.000   0.000 -1.00  0.00      U    O
> ATOM      4  N   MAC     0       0.123  -0.642   0.571  1.00  0.00      U    N
> ATOM      5  HT1 MAC     0       0.000   0.000   0.000 -1.00  0.00      U    H
> ATOM      6  HT2 MAC     0       0.000   0.000   0.000 -1.00  0.00      U    H
> ATOM      7  HT3 MAC     0       0.000   0..000   0.000 -1.00  0.00      U    H
> ATOM      8  CA  MAC     0      -5.107   1.352   1.005  1.00  0.00      U    C
> ATOM      9  HA  MAC     0       0.000   0.000   0.000 -1.00  0.00      U    H
> ATOM     10  N2  MAC     0      -4.299   0.713   1.207  1.00  0.00      U    N
> ...
> ...
>
> those occupency with -1 is troublesome and i need to remove them. any idea where i am going wrong?looking fwd for your suggestions.
> **NB. plz ignore if there is any double decimal...its somehow due to formatting**
>
>  
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