AMBER Archive (2003)

Subject: Re: AMBER: iam a newbie !!!

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Tue Sep 30 2003 - 04:12:43 CDT

It seems that you are missing an atom type!. Did you look at the pdb
file and try to spot where this atom lies? It seems that you you have a
residue called NH2 in your file ehich is strange if this a normal
protein. You probably have to identify this residue and see what's up
with it and then if necessary you have to set an atom type for this
atom. If you still have problems let me know and if nobody else replies
i will take a look at the file myself.
Vlad

 

Karthikeyan Pasupathy wrote:

>i tried to run a md for alpha conotoxin pdb id:1AKG
>
>i couldnt save amber parameters. I got a error like
>this :
>FATAL: Atom .R<NH2 17>.A<N 1> does not have a type.
>
>can anyone tell me why this happens and how to solve
>this problem please ....
>
>i used leaprc.ff94
>
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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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