Hi Anju,
your pdb file is in an odd format. It seems that the colums are not
sepereted far enough, so the atom name (and number, residuename, etc.)
are not in the place where antechamber expects them. If you closeley
look at the error output, you can see that entechamber assumes the M
from MTX to be part of the atomic name.Try to save your pdb file with a
different program, to get the proper spacing or do that by hand.
example:
ATOM 2 C 2 ? 2 0.488 -0.023 0.817 1.00 0.00
?1 C
yours:
ATOM 28 N28 MTX 1 3.593 -5.599 2.965
Benjamin
Anju Sharma schrieb:
>
> Hello Sir,
>
> While creating input files in antechamber, as directed by you, i
> encountered folllowing problem, where i am wrong? Hereby i am
> attaching Pdb file of the drug molexcule for your kind consideration.
> ----------------------------------------------------------------------------------------------------------------------------------------
> [root.amber exe]# /usr/local/amber8/exe/antechamber -i
> /usr/local/try/mtx2.pdb -fi pdb -o /usr/local/try/mtx2.prepin -fo
> prepi -c bcc -s 2
>
> Unrecognized atomic name M1, exit
> Unrecognized atomic name M2, exit
> Unrecognized atomic name M3, exit
> Unrecognized atomic name 4 M, exit
> Unrecognized atomic name 5 M, exit
> Unrecognized atomic name 6 M, exit
>
>
> Unrecognized atomic name 56 M, exit
> Unrecognized atomic name 57 M, exit
> Unrecognized atomic name 58 M, exit
> Unrecognized atomic name 59 M, exit
>
> Running: /usr/local/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Total number of electrons: 0; net charge: 0
>
> Running: /usr/local/amber8/exe/divcon
> Unable to find mopac charges in divcon.out
> Unrecognized atomic name 60 M, exit[root.amber exe]#
> ------------------------------------------------------------------------------------------------------------------------------
>
>
>
> --
> Anju Sharma
> Project Fellow,
> NIT, Hamirpur (H.P.)
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Received on Wed Aug 01 2007 - 06:07:31 PDT
