This example was used to import lipid bilayer coordinates from a collaborator, in a PDB format which included a single letter chain ID for each segment. By defining the PSF in advance to make the segment names match the chain ID, the PDB file can be read without splitting. (It is the READ SEQUence PDB command which really needs separate PDB files.) The PDB file looked like:
Code:
CRYST1   48.000   48.000   66.744  90.00  90.00  90.00 P 1           1
ATOM      1  N  ADPPCL   1      -8.355  -4.041  21.343  1.00  0.00      L    N
ATOM      2  C13ADPPCL   1      -8.577  -4.975  22.557  1.00  0.00      L    C
ATOM      3 H13AADPPCL   1      -8.571  -4.417  23.482  1.00  0.00      L    H
ATOM      4 H13BADPPCL   1      -7.835  -5.710  22.833  1.00  0.00      L    H
ATOM      5 H13CADPPCL   1      -9.543  -5.430  22.397  1.00  0.00      L    H
ATOM      6  C14ADPPCL   1      -9.604  -3.376  20.995  1.00  0.00      L    C
ATOM      7 H14AADPPCL   1      -9.726  -2.551  21.682  1.00  0.00      L    H
ATOM      8 H14BADPPCL   1     -10.447  -4.048  21.046  1.00  0.00      L    H
ATOM      9 H14CADPPCL   1      -9.631  -2.841  20.057  1.00  0.00      L    H
ATOM     10  C15ADPPCL   1      -7.274  -3.118  21.676  1.00  0.00      L    C
 :
 :
ATOM   9354 C315ADPPCL  72       9.893 -15.250  -0.998  1.00  0.00      L    C
ATOM   9355 H15XADPPCL  72      10.461 -16.091  -0.546  1.00  0.00      L    H
ATOM   9356 H15YADPPCL  72       8.794 -15.416  -1.014  1.00  0.00      L    H
ATOM   9357 C316ADPPCL  72      10.110 -13.947  -0.234  1.00  0.00      L    C
ATOM   9358 H16XADPPCL  72       9.553 -13.974   0.727  1.00  0.00      L    H
ATOM   9359 H16YADPPCL  72       9.695 -13.050  -0.740  1.00  0.00      L    H
ATOM   9360 H16ZADPPCL  72      11.211 -13.899  -0.097  1.00  0.00      L    H
ATOM   9361  OH2BTIP3W   1      21.131 -14.223  20.640  1.00  0.00      W    O
ATOM   9362  H1 BTIP3W   1      21.865 -14.195  20.025  1.00  0.00      W    H
ATOM   9363  H2 BTIP3W   1      20.495 -13.603  20.282  1.00  0.00      W    H
ATOM   9364  OH2BTIP3W   2      18.594  12.455  33.225  1.00  0.00      W    O
ATOM   9365  H1 BTIP3W   2      18.046  12.784  32.512  1.00  0.00      W    H
ATOM   9366  H2 BTIP3W   2      18.880  13.242  33.689  1.00  0.00      W    H

Here is the UNIVersal format used to read this file:
Code:
* define custom format for the lipid PDB files
*

read univ
* custom pdb
*
unknown
iseq  7 5
type 13 4
resn 18 4
segi 22 1
resi 23 4
x    31 8
y    39 8
z    47 8
w    61 6
titl  1 4 CRYS
excl  1 3 END
end

return

Finally, the script used to import the coordinates from the PDB file, and produce a COOR CARD file for subsequent use with CHARMM. The RESID option is used because the file does not contain absolute residue numbers, which are defined as both RESNO (Coordinate) and IRES (Universal) in io.doc, and as IRES in select.doc. The SEGID (chain ID) and RESID are enough to uniquely identify each atom in the PSF.
Code:
* import c27r coords
*

read rtf  card name protlpd27.rtf
read para card name protlpd27r.prm

read sequ dppc 72
gener L setup warn first none last none
read sequ tip3 2189
gener W first none last none noang nodihe

stream univfmt.str

read coor univ resid name dppc-c27r.pdb

write coor card name dppc-c27r.crd
* dppc c27r 1 microsec frame
*
stop



Rick Venable
computational chemist