AMBER Archive (2009)

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

From: Jio M (jiomm_at_yahoo.com)
Date: Sun Nov 01 2009 - 23:58:58 CST

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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