AMBER Archive (2003)

Subject: Re: AMBER: Fwd: Minimizing after solvation

From: Angela Pantelogianis (ap924_at_nyu.edu)
Date: Mon Jul 21 2003 - 10:26:30 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.

I DID CHANGE MY INPUT FILE TO RUN WITH SANDER. IT NOW LOOKS LIKE:

 &cntrl
  ntpr=10,
  ntf=1, dielc=1, scnb=2, scee=1.2, cut=10.0
  imin=1, maxcyc=5000, ncyc=50, ntb=1,
  ntr=1, igb=0,
 &end
 Group input for restraining DNA,Mg2+,Protein
 100
 RES 1 937
 END
END

THAT TOOK CARE OF THE ** failed to allocate pair array, bytes: -554087692 ERROR I WAS RECEIVING BEFORE, BUT NOW, WHEN RUNNING SANDER W/AMBER6, I AM GETTING THE ERROR
   1. RESOURCE USE:

 getting box info from bottom of parm
 getting new box info from bottom of inpcrd
 peek_ewald_inpcrd: SHOULD NOT BE HERE

>
> 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).

THIS WAS IN THE UNIX SHELL, AND I AM STILL HAVING THIS PROBLEM IN TRYING TO CREATE THE PDB FILE AFTER I ADDED THE SOLVENT. MY COMMAND WAS

broyde4 5% ambpdb -p phip_test_cio_wa.prmtop < phip_test_cio_wa.inpcrd > phip_test_cio_wa.pdb

  ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES

THE PRMTOP AND INPCRD FILES WERE FROM THE TLEAP, WHICH RAN WITH NO ERRORS.

THANK YOU FOR YOUR HELP AND SORRY FOR THE CONFUSION IN MY FIRST EMAIL.

ANGELA

 ..good luck...dac

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