Dear Amber users,
Sorry for long mail
I was just comparing two cases. using HF method I minimised my residue having a methyl cap( which I want to remove later while joining with other second residue). After esp calcualtions and using -a flag in respgen method I forced the charge on CH3 group to be zero by preparing .in file
I used following
respgen -i my.ac -o my.respin1 -f resp1 -a my.in
respgen -i my.ac -o my.respin2 -f resp2 -a my.in
I was able to get a overall neutral residue (0.0000 charge) with cap (CH3) itself having net charge of C,H,H,H be zero also.
I think the charges were generated on each atom to be RESP type (please correct me)
�BUT if I just take esp.out file from gaussian for the same residue and use it with antechamber:
antechamber -i my_esp.out -fi gout -o my.mol2 -fo mol2 -c resp
{ALSO we can do same thing on respgen without using -a flag ,results will be same as for antechamber}
I get charges on each atom on residue which is highly� different from charges so obtained by using -a flag.
MY main query is I want to build large molecule with the� CH3 capped residue and study its dynamics interaction with some organic molecule (RESP charges with antechamber). Will it be OK to use charges so obtained from -a flag in respgen ( forcing charge on cap be zero) because I have no other choice and studying its interaction with organic molecule having charges derived without -a flag (which is also not required)
Please suggest me.
thanks,
JIomm
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Received on Fri Oct 30 2009 - 07:00:02 PDT
