VMD-L Mailing List

From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Tue Sep 13 2005 - 11:50:04 CDT

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 (www.charmm.org <http://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 <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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