AMBER Archive (2003)

Subject: Re: AMBER: Fwd: Minimizing after solvation

From: David A. Case (case_at_scripps.edu)
Date: Sat Jul 19 2003 - 23:34:53 CDT

On Fri, Jul 18, 2003, Angela Pantelogianis wrote:
>
> I am running minimization on an RB69-PhIP system. I have already added Na+
> ions and ran one minimization holding the main chain atoms still. I created
> a pdb file from the restrt file after minimization and reloaded it into
> tleap. I then solvated the system by using
>
> solvateBox WATBOX216 10.0

I assume the above is a typo, has the wrong number of arguments.

>
> Everything went fine, and I then saved the new coordinates and parameters
> under .prmtop and .inpcrd
>
> The files saved with no errors.
>
> My next step was to minimized the system by holding the system still and
> equilibrating the solvent and ions. Here is my input file for
> sander_classic:

You should not be running sander_classic for periodic systems. Since you
didn't set ntb in your input, it may not even recognize it as a periodic
box....Also, you probably don't want a distance-dependent dielectric
when you have explicit solvent. Try using sander and set ntb.

>
> My second problem came when I tried to create a new pdb file with the added
> solvent included. It gave me the error:
>
> ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES

What is "it" that gave you this error? Please follow the advice about
reporting bugs: instead of telling us what your intentions were ("I tried
to create a new pdb file"), tell us instead as precisely as you can what
you really did (what commands you used, what the arguments were).

..good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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