Hi,
On Thursday, 17. April 2008 17:02, uccabke.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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Greetings,
Florian
--
-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 18 2008 - 21:20:05 PDT
