AMBER Archive (2009)

Subject: Re: [AMBER] charge not zero on group: RESP

From: Ben Roberts (roberts_at_qtp.ufl.edu)
Date: Sat Jul 18 2009 - 07:45:10 CDT

Hi Jiomm,

> I am trying to give net charge on terminal group(--COCH3) to be
> zero,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 had the same problem just yesterday, in fact. I solved it by checking
the .respin1 file. I had made the mistake of over-defining my groups in
the supplementary resp file (your eda_v.in). I had put _every atom in a
charge group, and it didn't like that - it wanted at least some atoms to
fall outside a charge group.

So you may want to check your .respin1 file, in case it's doing things
you don't expect. If you're still fighting with it, it may be worth
including that file as an attachment here on the list (as well as the
eda_v.in and eda_v_esp.ac).

Regards,

Ben

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