From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Thu Sep 18 2008 - 09:34:14 CDT

the extra decimal points (i dont know how n why) comes when i copy the file in the mail...its not present in the original pdb file.
guess the problem is with the naming....let me check and i ll tell (or bother) you
regards

 

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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, 18 September, 2008 5:48:15 PM
Subject: Re: vmd-l: psfgen problem
Hi Rudra,
the atom names in the pdb need to match up with the names (second 
column) in the topology entry, not the types (third column).
Also, if you look at your pdb  file you'll note that you still have some 
extra decimal points and other places where the columns aren't properly 
aligned.
Peter
Rudra Banerjee wrote:
> hello friends,
> plz forgive me for resending the same file. actually the molecule structure was craped due to the missing tab formating . so i am resending it with corrected structure
> i am trying to generate osf file for acridine orange with the initial coordinate file:
>
> #CRYST1    0.000    0..000    0.000  90.00  90.00  90.00 P 1           1
> ATOM      1  CA   MAC A  1      -3.039   1.934  -0.283  1.00  0.00           C
> ATOM      2  CA   MAC A  1      -3.189   0.892   0.625  1.00  0.00           C
> ATOM      3  CA   MAC A  1      -2.112   0.042   0.894  1.00  0.00           C
> ATOM      4  CA   MAC A  1      -0.879   0.204   0.276  1.00  0.00           C
> ATOM      5  CA   MAC A  1      -0.733   1.261  -0.643  1.00  0.00           C
> ATOM      6  CA   MAC A  1      -1.812   2.120  -0.917  1.00  0.00           C
> ATOM      7  NR2  MAC A  1       0.123  -0.642   0.571  1.00  0.00           N
> ATOM      8  CA   MAC A  1       1.315  -0.482  -0.029  1.00  0.00           C
> ATOM      9  CA   MAC A  1       1.562   0.544  -0.962  1.00  0.00           C
> ATOM     10  CA   MAC A  1       0.512   1..419  -1.262  1.00  0.00           C
> ATOM     11  CA   MAC A  1       2.353  -1.354   0.273  1.00  0.00           C
> ATOM     12  CA   MAC A  1       3.613  -1.234  -0..321  1.00  0.00           C
> ATOM     13  CA   MAC A  1       3.854  -0..212  -1.232  1.00  0.00           C
> ATOM     14  CA   MAC A  1       2..827   0.670  -1.563  1.00  0.00           C
> ATOM     15  NH2  MAC A  1       4.671  -2.189   0.006  1.00  0.00           N
> ATOM     16  NH2  MAC A  1      -4.299   0.713   1.207  1.00  0.00           N
> ATOM     17  HP   MAC A  1      -3.879   2.612  -0.492  1.00  0.00           H
> ATOM     18  HP   MAC A  1      -2.248  -0.784   1.607  1.00  0.00           H
> ATOM     19  HP   MAC A  1      -1.685   2.949  -1.629  1.00  0..00           H
> ATOM     20  HP   MAC A  1       0.669   2.239  -1.978  1..00  0.00           H
> ATOM     21  HP   MAC A  1       2.175  -2.167   0.992  1.00  0.00           H
> ATOM     22  HP   MAC A  1       4.846  -0.106  -1.696  1.00  0.00           H
> ATOM     23  HP   MAC A  1       3.013   1.474  -2.290  1.00  0.00           H
> ATOM     24  CA   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  CA   MAC A  1      -4.392  -0.073   1.897  1.00  0.00           C
> ATOM     27  HP   MAC A  1       6.081  -1.136  -0.148  1.00  0.00           H
> ATOM     28  HP   MAC A  1       5.550  -2.185  -1.527  1.00  0.00           H
> ATOM     29  HP   MAC A  1       6.270  -2.939  -0.032  1.00  0.00           H
> ATOM     30  HP   MAC A  1      -4.830   2.397   1.270  1.00  0.00           H
> ATOM     31  HP   MAC A  1      -5.986   1.045   1.614  1.00  0.00           H
> ATOM     32  HP   MAC A  1      -5.354   1.307  -0.080  1.00  0.00           H
> ATOM     33  HP   MAC A  1      -5.425  -0.085   2.310  1.00  0.00           H
> ATOM     34  HP   MAC A  1      -4.187  -1.041   1.386  1.00  0.00           H
> ATOM     35  HP   MAC A  1      -3.663   0..071   2.725  1.00  0.00           H
> ATOM     36  CA   MAC A  1       4.407  -3.273   0.925  1.00  0.00           C
> ATOM     37  HP   MAC A  1       3.586  -3.909   0.524  1.00  0.00           H
> ATOM     38  HP   MAC A  1       5.323  -3.895   1.040  1.00  0.00           H
> ATOM     39  HP   MAC A  1       4.096  -2.858   1.910  1.00  0.00           H
> END
> and since it is not supplied in charmm force field, i have generated one for this..the corresponding part looks like:
> !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
> BOND  N2 CA CA HA1 CA HA2 CA HA3 N CB CB HB1 CB HB2 CB HB3
> BOND  CD1 HD1 CE1 HE1 C1 H1 C4 H4 C5 H5 C7 H7 CD2 HD2
> 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
> IMPR N C CA HN  C CA 
> DONOR  N  N1 N2
> ACCEPTOR CA CB CE2 C3 C8 C9  
>
> IC s are not given as i have supplied all the coordinates in the pdb file. but it is not of much help.
> can you people suggest me where i am going wrong?
>          
>
>
>  
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