AMBER Archive (2008)

Subject: Re: AMBER:

From: Florian Haberl (Florian.Haberl_at_chemie.uni-erlangen.de)
Date: Thu Apr 17 2008 - 10:17:24 CDT

Hi,

On Thursday, 17. April 2008 17:02, uccabke_at_ucl.ac.uk wrote:
> Hi Amber users
>
> I have a pdb file of a protonated protein. When I load this molecule into
> xleap, it adds further H atoms, I do not understand why this happened? (my
> molecule is already containing the necessary number of H atoms for which I
> only need to create inpcrd and prmtop files). But since xleap added further
> H atom types, it complains when I want to create prmtop and inpcrd files
> such as:
>
> lots of lines like this:
> FATAL: Atom .R<HIE 794>.A<2HB 18> does not have a type.
> FATAL: Atom .R<HIE 794>.A<3HB 19> does not have a type.
> FATAL: Atom .R<HIE 794>.A<OXT 20> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>

AMBER is using different names for different protonation state of Histidine
residue:

     |Histidine, delta H HID |
     |Histidine, epsilon H HIE |
     |Histidine, protonated HIP |

I don`t know which kind of protonation state you want. You only have to change
the residue names in your pdb file.

>
> any help on how to create promtop and inpcrd for an already protonated and
> ready pdb file is much appreciated.
> Regards
> Boutheina
>
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Greetings,

Florian 

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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