Dear J. Wang,
I think I am not able to present my query well, I will now try to make it more clear.
I have three residues being capped. The cap was constrained to have
zero charge and want to use three repeating residues to make big
molecule by removing the caps so that I ultimately get zero charge on
big molecule. The big molecule is to be interacted with some organic
molecule (whose charges are derived by RESP method)
The charges were different on atoms if derived with constrained (
forcing charge to be zero on cap ) or non-constrained method, as you
have replied also
What method should I use for the organic molecule which is to be
finally interacted with big molecule (having repeating residues'
charges being derived from non constrained method)
1) should I look for SQRT values no matter constraint or non-constraint
method is used. What should be upper limit for the value?
2) if constraint is to be used for organic molecule (which is to
be interacted with big molecule) then will I have to include all the
atoms in constraint .in file (-a flag)
please help me to understand this.
thanks and regards,
JIomm
--- On Mon, 11/2/09, Junmei Wang <junmwang.gmail.com> wrote:
From: Junmei Wang <junmwang.gmail.com>
Subject: Re: [AMBER] Re: RESP with -a and witout -a flag
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Monday, November 2, 2009, 4:48 PM
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.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.yahoo.com> wrote:
>
> From: Jio M <jiomm.yahoo.com>
> Subject: [AMBER] Re: (files attached) RESP with -a and witout -a flag
> To: "amber" <amber.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.gmail.com> wrote
> From: Junmei Wang <junmwang.gmail.com>
> Subject: Re: [AMBER] RESP charges with -a and without -a flag
> To: "AMBER Mailing List" <amber.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.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.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> >
>
>
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Received on Tue Nov 03 2009 - 23:00:02 PST
