Hii;
This seems to be an issue with isoleucine. Try deleting all hydrogens from
those residues. You can use reduce, trim option to do that. Leap will
automatically add them back.
I think the problem is that Leap doesn't find CD 20 as atom from its amino
acid library. You can try to check the amino acid library located at
$AMBERHOME/dat/leap/lib/all_amino94.lib
Modify accordingly if you can or try from scratch. Sometimes leap unable to
map the amino acids because of bad type such as CD 20 CG 20 etc.
Try deleting all hydrogens from the receptor using Chimera, Reduce or any
other programme and re run the leap again.
All d best.
On Tue, Apr 8, 2014 at 8:05 AM, Arunima Shilpi <writetoash28.gmail.com>wrote:
> Dear sir
>
> Presently I am studying Protein-Ligand interaction in which one of the
> resuide has been mutated to ILE. While saving the co-ordinates it shows the
> following error
>
> FATAL: Atom .R<ILE 709>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 731>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 752>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 766>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 828>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 835>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 899>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 923>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 942>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 974>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 977>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 980>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 995>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 997>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1020>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1114>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1121>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1145>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1147>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1268>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1269>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1308>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1319>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1340>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1362>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1367>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1382>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1396>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1446>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1519>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1538>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 1542>.A<CD 20> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> I request you to kindly guide me in debugging the error
>
> Regards
>
> Arunima
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Tue Apr 08 2014 - 00:30:02 PDT
