AMBER Archive (2003)

Subject: Re: AMBER: problem with pdb files

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Oct 13 2003 - 03:35:04 CDT

Well, there is a certain pdb format which :Leap accepts. Ususally this
format is made compatible with the PDB data base format in the leaprc
file. I dont know how your file looks lile so I cannot say exactly
what's the problem....you can test it by taking a pdb (from the data
base) file and load it into leap ..then save topology and crd file and
transform them into pdb file with ambpdb (with -aatm option)...then you
will get a tipical Amber pdb file and then you can compare it with your
file.
Hope this helps,
vlad

Mithun Mitra wrote:

>Hi,
> I am a new user of amber program. I made a protein-rna complex
>structure using FTDOCK which gave me the pdb file of the complex as the
>output. I loaded the pdb file in the leap module of amber. After that I
>gave the command for creating parameter files and coordinate files . I
>gave me error and files were not created.
> Is there any problem with directly inputting the pdb files?
> Is there any quick way of editing the pdb files ?
>Thanks,
>Mithun
>
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-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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