AMBER Archive (2006)

Subject: RE: AMBER: About tleap

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jan 12 2006 - 14:08:14 CST

Dear Varsha

> when i run tleap for a protein where i changed three
> of HID redues and added one Zn ion, i am getting my
> perturbed and unperturbed charge to be -2 and -4
> respectively. I dont know which charge should i
> consider for neutralizing my protein. I have read few
> threads from mail archive but i don't want to do any
> change in xleap system files itself.
> Any comments or suggestion??

Assuming you want to run regular MD the unperturbed charge is the one you
are interested in. The perturbed charge is ignored when writing a regular
prmtop file using saveamberparm.

This is also the charge you should use for neutralisation. You should check
yourself to make sure -2 is the charge you expect. Add up the charges of all
charged residues and the resp charge you have added for the zinc and make
sure it gives what you expect.

The perturbed charge is only used for doing free energy perturbation and is
only used when you specify saveamberpertparm. The reason you are seeing the
perturbed charge = -4 and the unperturbed = -2 I suspect is because the
perturbed charge was never defined for the zinc ion and so defaults to 0
instead of +2. For regular MD you can safely ignore the perturbed charge
value.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Varsha Goyal
> Sent: Thursday, January 12, 2006 10:28
> To: amber_at_scripps.edu
> Subject: AMBER: About tleap
>
> Hello,
> when i run tleap for a protein where i changed three
> of HID redues and added one Zn ion, i am getting my
> perturbed and unperturbed charge to be -2 and -4
> respectively. I dont know which charge should i
> consider for neutralizing my protein. I have read few
> threads from mail archive but i don't want to do any
> change in xleap system files itself.
> Any comments or suggestion??
> Thanks,
> Varsha
>
>
>
>
>
>
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