AMBER Archive (2009)

Subject: Re: [AMBER] RE: charge not zero on group:''''.respin1 attached

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sun Jul 19 2009 - 02:41:17 CDT

Dear Jiomm,
               
> Thanks BEN for the reply but I didnt understand fully what you
> suggested. Now I have attached .respin1 file also {note I have removed
> one blank line space as it was suggested in archive}

This eda_v.respin1 input seems correct.

You also need to create the second RESP input, recomputing the charges
of the 2 methylene groups and freezing the atoms involved in the
intra-molecular charge constraint & those of the NH2 group.

You might read:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
section "General information about charge fitting"

You might also look at the F-1 project in R.E.DD.B.
http://q4md-forcefieldtools.org/REDDB/projects/F-1/
& the corresponding RESP inputs
However, this F-1 R.E.DD.B. project is a little more complicated than
yours & you will find nmol=4 structures (4 orientations; as nmol > 1
in this case, we need to jump a line before defining the
intra-molecular charge constraints). As you can see there are several
intra-molecular charge constraints defined in the 1st RESP input. All
the corresponding charge values are frozen in the second RESP stage,
while the charges of the methyl groups are recomputed & equivalenced
in the second RESP stage (You do not need to define an
"Inter-molecular charge equivalencing" section in your case as nmol=1).

I hope this helps.

regards, Francois

>> I am trying to give net charge on terminal group(--COCH3) to
>> bezero,being capped on residue's N terminal (is it correct to do
>> like this
> if not pls correct me):
>                                    
> NH2-CH2CH2-NH--COCH3
>
>> 1) I optimised capped residue with hf/631+ g( d ) also esp derived
>> on same basis and got eda_v.esp (sorry I cant attach this file : it
>> cross the limit of mail size 2083 kb)
>
>> 2) I read in archive that .respin1 and .respin2 files should be
> corrected by removing blank line.I corrected it also for .respin1
>
>> 3) I have constrained the group charge to be zero by eda_v.in file
>> (pls try to have a look on it)
>
>> 4) but I am not getting net charge on --COCH3 to be zero, though
>> net charge on residue is zero
>
>> 5) reason can be that I am using only one conformation; but I think >it
> should not matter because I am using constraint on group charge >to be
> zero (pls correct me)
>
>> I used following with -a flag :
>> respgen -i eda_v_esp.ac -o eda_v.respin1 -f resp1 -a eda_v.in
>
>> gedit eda_v.respin1
>> respgen -i eda_v_esp.ac -o eda_v.respin2 -f resp2
>
>> resp -O -i eda_v.respin1 -o eda_v.respout1 -e eda_v.esp -t >qout_stage1
>
>> resp -O -i eda_v.respin2 -o eda_v.respout2 -e eda_v.esp -q
>> >qout_stage1 -t qout_stage2
>
>> antechamber -i eda_v_esp.ac -fi ac -o eda_v.mol2 -fo mol2 -c rc
>> >-cf qout_stage2
>
>> pls suggest the missing things or this method cannot be used at >all
>
> thanks
> Jiomm

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