AMBER Archive (2009)

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

From: Jio M (
Date: Sat Oct 31 2009 - 00:13:03 CDT

Dear J. Wang,

I am attaching the mol2 files

1) with_a_flag.mol2 {prepared by respgen and resp module using -a flag}

here CH3 has zero charge and overall charge is also zero

2) without_a_flag.mol2 {done by using esp.out file from Gaussian and
antechamber or else can be done with respgen also but without -a flag }

I  just wanted to see difference  in methods  by using
-a flag or  without using  -a flag  on this residue.
Also I have to have use -a flag because I need to force zero charge on
caps (here methyl) because they ultimately have to be removed while
joining with other residues

 I want to make  big molecule using this residue and study
its interaction with organic molecule having charges derived with resp
method. please suggest and correct me



--- On Fri, 10/30/09, Junmei Wang <> wrote:

From: Junmei Wang <>
Subject: Re: [AMBER] RESP charges with -a and without -a flag
To: "AMBER Mailing List" <>
Date: Friday, October 30, 2009, 4:49 PM

Hi, JIomm
How big is the difference?  Could you attach the files? The net charge of
-CH3 group should close to zero in most situation.



On Fri, Oct 30, 2009 at 8:36 AM, Jio M <> wrote:

> 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.
> thanks,
> JIomm
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