Subject: still need help: pdb --> charmm

From: "J. Zheng" <[email-masked]>
Date: Wed, 30 Jan 2002 17:10:06 -0800 (PST)

hi, CCLer:

   First of all, I would like to thank all of you who give me suggestion
and technical suuport. I really appreciate it.

   My research is molecular modeling of protein adsorption. What I want is
to get initial configuration from PDB, then convert to Charmm Format.
It is only way that I can use CHARMM force field. So, from charmm program,
I want to get

  1) COOR file which includes atomtype of charmm.
  2)  PSF file which includes connectivity table.

   Based on these two files, I will code by myself for a speicfic protein
adsorption. In order to do this project, our group purchase CHARMM. But
nobody know how to use it. That is why I ask you guys for helping.

  After 2 days, I have got prelimitary results. But I don't know whether
it is right. If correct, I will summary what I do and what you guys
suggested later. otherwise, I have to still struggle on this conversion.

-------------------------------------------------------------------------

 1. Charmm program

   suggested by Torsten Becker <[email-masked]>
                Xiang(Simon) WANG <[email-masked]>
                Marcin Krol <[email-masked]>
                Dr. Richard L. Wood <[email-masked]>
                Szilveszter Juhos <[email-masked]>

   following I will list COMMAND I inputed. (based on Becker's script)

   ok   1) * Emacs generated Charmm Inputfile
           *

   ok   2) bomlev 0 (i don't know what means of this command though)

   ok   3) open read unit 1 card name
           /charmm/c27b4/toppar/top_all22_prot.inp
           read rtf card unit 1
           close unit 1

   ok   4) open read unit 1 card name
           /charmm/c27b4/toppar/par_all22_prot.inp
           read param card unit 1
           close unit 1

    -----------------------------------------------------------
           when I read param card unit 1, screen prints lots of
information as following format

 PARRDR> Multiple terms for dihedral type: INDEX 99 CODE 1369603 CT2
-SM -SM -CT2
 PARRDR> Multiple terms for dihedral type: INDEX 98 CODE 1369603 CT2 -SM
-SM -CT2
 PARRDR> Multiple terms for dihedral type: INDEX 96 CODE 1367651 CT2 -C
-NH1 -CT2
  ------------------------------------------------------------------

            I was supposed that it is right.

   ok??  5) open read unit 1 card name "7lyz.pdb"
             read sequ pdb unit 1
             close unit 1

          ------charmm gives this information------

  ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 18 TITRATABLE GROUPS
 THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND
RTF
  HIS - 0 ASP - 7 GLU - 2 LYS - 6 TYR - 3

  what does it means?

         --------------------------------------------

   ok??  6) generate 7lyz

    -------------------------------------
 CHARMM> generate 7lyz
 THE PATCH 'NTER ' WILL BE USED FOR THE FIRST RESIDUE
 THE PATCH 'CTER ' WILL BE USED FOR THE LAST RESIDUE
 GENPSF> Segment 1 has been generated. Its identifier is 7LYZ.
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments = 1 Number of residues = 129
         Number of atoms = 1968 Number of groups = 586
         Number of bonds = 1988 Number of angles = 3547
         Number of dihedrals = 5183 Number of impropers = 351
         Number of HB acceptors = 186 Number of HB donors = 271
         Number of NB exclusions = 0 Total charge = 8.00000
    -----------------------------------------------

   not ok  7) open read unit 1 card name "7lyz.pdb"
              read coor pdb unit 1
              close unit 1

--------------------------------------------------
 ** WARNING ** For atom in coordinate file, the corresponding residue in
the PSF lacks that atom:
 INDEX= 996 IRES= 129 RESID=129 RES=LEU ATOM=O
 ** WARNING ** After reading, there are no coordinates for selected atom:
2 1 LYS HT1
 ** WARNING ** After reading, there are no coordinates for selected atom:
3 1 LYS HT2
 ** WARNING ** After reading, there are no coordinates for selected atom:
4 1 LYS HT3
 ** WARNING ** After reading, there are no coordinates for selected atom:
6 1 LYS HA
 ** WARNING ** After reading, there are no coordinates for selected atom:
8 1 LYS HB1
 ** WARNING ** After reading, there are no coordinates for selected atom:
9 1 LYS HB2
 ** WARNING ** After reading, there are no coordinates for selected atom:
11 1 LYS HG1
 ** WARNING ** After reading, there are no coordinates for selected atom:
12 1 LYS HG2
 ** WARNING ** After reading, there are no coordinates for selected atom:
14 1 LYS HD1
 ** WARNING ** After reading, there are no coordinates for selected atom:
15 1 LYS HD2
 ** A total of 970 selected atoms have no coordinates
 *** LEVEL 2 WARNING *** BOMLEV IS 0
---------------------------------------------------------------------

    ok??  8) open write unit 2 card name "a.crd"
             write coor unit 2 card
             * 7lyz coor
             *
             close unit 2

-------------------------------------------------------
CLOLGU> *****
WARNING ***** Attempt to close unit that was not open.
---------------------------------------------------------------

    ok??  9) open write unit 3 card name "a.psf"
             write psf unit 3 card
             * 7lyz psf
             *
             close unit 3

 =================================================================

   RESULTS:

   I have check a.crd and a.psf file. I found that there are 1968 atoms.
Compared with original 1000 atom of 7lyz.pdf, there are more 968 atom in
a.crd and a.psf files. and some atoms don't have coordinate since the
coordinates were labelled 9999.0000..

   That is what I done. I felt these initial configurature may not be
right. I have to resort to you guys.

   thank for your patience to read this verbose email.

  jie