VMD-L Mailing List

From: Sergio Anis (sergioanis_at_ispwest.com)
Date: Tue Sep 13 2005 - 12:26:12 CDT

        find the parameters for the hem is my second stage, to do that, first i need to
'form' the complex protein-hem (it is not a regular hem, so i wont find it in charmm).

        So, this explain why the script 'mergepdbs' doesn't work, any suggestion why putting
the file together is not working either?

        Theoretically, if i give any pdb containing the coordinates of a protein with a
heteroatom, vmd (or any visualization software) should be able to show me the structure,
right?

        thanks,

        Sergio

         

         

        This is because you are trying to build a residue for which
1) there are not parameters

2) It is not defined as a residue

As I can see from your mail you try to load a protein with a HEM group.
Psfgen can
only build a psf from residues defined in the topology file
you used. Charmm22 have
defined every aminoacid, charmm27 also
have definitions for lipids. Every molecule
you want to use have to be
defined in that file. As far as i know, There is not
a HEM residue in
CHArmm. That is why this error is evoqued:

unknown residue type HEM

You may search into Charmm web site ( [http://www.charmm.org] www.charmm.org ) because
I remember
someone defined a topology for HEM group some time ago. A good start
to
get clarity on this issue is the tutorial in namd site about how
to parametrize
a novel residue.

Leonardo

On 9/12/05, Sergio Anis < [mailto:sergioanis_at_ispwest.com]sergioanis_at_ispwest.com
>wrote:
hi everybody;

I'm having problems writing a pdb file. First, let me tell you what I'm
doing:

1) load 2 molecules (mol1: 'protein + heteroatom1'; mol2: 'heteroatom2')
2) align 'heteroatom1' and 'heteroatom2'

3) write a pdb file with the coordinates of 'protein + heteroatom2'

That is: replacing heteroatom1 by heteroatom2

Here is what I tried:

1) write a pdb with the coordinates of 'protein' and another pdb with the

coordinates of 'heteroatom2'
2) use the script 'mergepdbs.tcl'
I get this error message:

building segment V1
setting patch for first residue to NONE
setting patch for last residue to NONE
reading residues from pdb file mimic2.pdb
unknown residue type HEM
extracted 1 residues from pdb file
Info: generating structure...
unknown residue type HEM
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

Another approach:
1) manually paste heteroatom2 at the end of protein (making the appropriates
changes like TER by END -at the end of the protein- and keep adding the
number of the atom -the number right after the word HETATM-; at one point I

even added the CONECT info for the heteroatom)
When I load this pdb file I don't get the heteroatom. I get the following
messages (several time each):

error> residue exceeded maximum number of bonds (4)

warning> unusual bond between residues .... and ....

But if I open protein or heteroatom2 alone I don't have any problem

I appreciate any advice you can give me

thanks,

Sergio
  

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~
Leonardo Andres Sepúlveda Durán
Graduado de Bioquimica
Universidad de Chile
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Manuel Antonio Maira 987 depto. # 302
Providencia
Santiago
Chile
Codigo postal: 752-0249
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