[AMBER] using Mg with ff99SB

From: Irene Newhouse <einew.hotmail.com>
Date: Thu, 30 Jun 2011 11:24:20 -1000

I'm trying to do MD of a protein complexed with Mg-ATP, and I'm having difficulty processing the MG through tleap. I'm using prepi/frcmod files for ATP from the work of Carlson & al, which was recently discussed on this mailer [thanks so much!] From grepping around the /dat/leap dirs of amber11, I've deduced that the atom name for MG should be MG2. But I have no idea what to call the residue name. I've tried:

 HETATM 3092 MG2 IP D 206 32.173 43.347 19.203 0.50 27.35 Mg2+

and I've tried leaving the residue name field blank. Both instances result in the same leap message [with IP replace by spaces in the other case]:

Creating new UNIT for residue: IP sequence: 206
Created a new atom named: MG2 within residue: .R<IP 206>

When I try to write prmtop/inpcrd files at the end of my processing, I get:
FATAL: Atom .R<IP 206>.A<MG2 1> does not have a type.
Failed to generate parameters
Parameter file was not saved.

Yes, I did load the forcefield [I work from pre-written scripts as much as I possibly can, since I'm prone to stupid typing errors]. What do I do now? Thanks!

Irene Newhouse

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Received on Thu Jun 30 2011 - 14:30:04 PDT
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