Subject: Re: CCL:PDB file structure

From: David van der Spoel <[email-masked]>
Date: Thu, 31 May 2001 09:08:54 +0200 (CEST)

On Thu, 31 May 2001, Sergio Manzetti wrote:

>Hi everyone. I have recently understood that many Protein programs don't
>understand a PDB file with only the ATOM and CONECT records. I am attempting to
>dock ligands to a modelled molecule that unfurtunately is not accepted by the
>software (AUTODOCK). Do you have knowledge to which other records are relevant
>for such procedures?
You should be a bit more specific. What exactly does Autodock not like?
Many program neglect the conect records, since they are usually absent
anyway most programs have a database. Anyway, with autodock you do get the
source code, so it should be quite easy to see where the problem is.
Alternatively you grab a pdb file from the pdb databank, compare it to
your own and modify your own accordingly.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel		Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: [email-masked]	www: http://zorn.bmc.uu.se/~spoel
phone:	46 18 471 4205		fax: 46 18 511 755
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From: Hetenyi Csaba <[email-masked]>
Date: Thu, 31 May 2001 02:28:17 -0700 (PDT)

> >software (AUTODOCK). Do you have knowledge to which other records are relevant

Hi,
AutoDock does not need the CONNECT records of the target, only 
ATOM/HETATM records.
Csaba