AMBER Archive (2009)

Subject: [AMBER] RESP charges with -a and without -a flag

From: Jio M (
Date: Fri Oct 30 2009 - 08:36:43 CDT

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 -o my.respin1 -f resp1 -a
respgen -i -o my.respin2 -f resp2 -a

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.


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