AMBER Archive (2009)

Subject: Re: [AMBER] Re: RESP with -a and witout -a flag

From: Junmei Wang (junmwang_at_gmail.com)
Date: Mon Nov 02 2009 - 10:48:48 CST

Hi, JIomm
The charges of NH2 do have a significant difference. I checked the
SQRT(chipot/ssvpot) values for the two RESP fittings, the free resp fitting
is 0.27 and the constrained is 0.40. This means the constrained one has a
little bit worse fitting performance. I think it may be OK to use the
constrained charges. It is a good idea to make a comparison on the binding
energies for both charge sets.

Best

Junmei

On Sun, Nov 1, 2009 at 11:58 PM, Jio M <jiomm_at_yahoo.com> wrote:

> Dear J. Wang,
>
>
>
> Sir, I have sent the attached files two days before. If I didn't present
> my query well please let me know and Sorry for being impatient for the
> reply.
>
>
>
> I want to know whether I can use two molecules ,interacting with each
> other, having charges derived by using -a and without using a flag
> (respgen) because of the reasons stated in previous mail
>
>
>
> thanks,
>
> JIomm
>
> --- On Sat, 10/31/09, Jio M ><jiomm_at_yahoo.com> wrote:
>
> From: Jio M <jiomm_at_yahoo.com>
> Subject: [AMBER] Re: (files attached) RESP with -a and witout -a flag
> To: "amber" <amber_at_ambermd.org>
> Date: Saturday, October 31, 2009, 5:17 AM
>
> Dear J. Wang,
> Sorry I didnt attached files previously
>
> 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
> thanks
> JIomm
> --- On Fri, 10/30/09, Junmei Wang <junmwang_at_gmail.com> wrote
> From: Junmei Wang <junmwang_at_gmail.com>
> Subject: Re: [AMBER] RESP charges with -a and without -a flag
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> 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.
> Best
> Junmei
>
> On Fri, Oct 30, 2009 at 8:36 AM, Jio M <jiomm_at_yahoo.com> 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 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> _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> >
>
>
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