I suggest
Please check the number of bonds attached to the molecule, and check the
proper arrangement of the H bonds, you can use argus Lab for adding the
missing no. of H bonds without changing the orientation of the molecule
*Akash Deep Biswas*
*Int. M.Sc in BioScience and Bio-Informatics*
*Xth Semester, Roll No: BBI10012*
*MBBT, Tezpur University*
*Tezpur, Assam-784028*
*Ph- +918876088695, +919864461811.*
On Tue, Mar 3, 2015 at 5:05 PM, Swithin Hanosh <swithinhanosh.gmail.com>
wrote:
> Dear Hannes Loeffle ,
>
> Thanks for the reply. I removed the CONECT information from the pdb
> file, but now i recieved the following error :
>
> " Running: /home/damp/amber14/amber14/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> Info: Bond types are assigned for valence state 6 with penalty of 2
>
> Running: /home/damp/amber14/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0
> -o ANTECHAMBER_AC.AC -p gaff
> Total number of electrons: 203; net charge: 0
> INFO: Number of electrons is odd: 203
> Please check the total charge (-nc flag) and spin multiplicity (-m
> flag)
>
> Running: /home/damp/amber14/amber14/bin/sqm -O -i sqm.in -o sqm.out
> Error: cannot run "/home/damp/amber14/amber14/bin/sqm -O -i sqm.in -o
> sqm.out" of bcc() in charge.c properly, exit "
>
>
> after running the command : " antechamber -i sam-in-h.pdb -fi pdb -o
> sam.mol2 -fo mol2 -c bcc -s 2 ". The output generated is attached with
> the mail. Please explain the source of error.
>
> Thank You,
> Swithin Hanosh
>
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Received on Tue Mar 03 2015 - 04:00:03 PST
