AMBER Archive (2007)

Subject: AMBER: Defining BOX INFO during TLEAP

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Mon Jan 22 2007 - 21:02:15 CST

Dear Friends

This might sound like a basic question:

I have the PDB file of lipid-protein-ligand-water system which I want
to load using TLEAP and write corresponding PRMTOP INPCRD files for
doing simulation in AMBER 8.

I want to do these simulations using PBC (NPT). While doing
minimization, I got the following message >>>

-----------------------------------------------------------------------------------------------------------------------
| Flags: MPI
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info not found in inpcrd
|Largest sphere to fit in unit cell has radius = *********
-----------------------------------------------------------------------------------------------------------------------

Can somebody please tell me if we do not use TLEAP to solvate system
(e.g. using solvateoct command), then what is the procedure of
defining the BOX Info in the INPCRD and PRMTOP files?

My Input file looks like this >>>>>

AT1 Telmi in DMPC Water and Ions: Initial Minimisation for water + ions
 &cntrl
  imin = 1,
  maxcyc = 5000,
  ncyc = 1000,
  ntb = 1,
  ntr = 1,
  cut = 10
 /
Hold the AT1 Telmi and Lipids fixed
500.0
RES 1 495
END
END

Best Regards, -Akshay Patny (Olemiss)

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Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17_at_olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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