[AMBER] problem on running saveAmberParm

From: tianyuan meng <oceanrabbit.mty.gmail.com>
Date: Fri, 23 Apr 2010 09:54:39 +0800

 Hi all,
I am a freshman on AMber and I am running the Tutorial on loop dynamics of
HIV-1 integrase core domain. There is something wrong when I tried to run

The program reads:

> source leaprc.ff03
> mol=loadpdb wt1mg_water.pdb
Loading PDB file: ./wt1mg_water.pdb
-- residue 1: duplicate [2H] atoms (total 2)
   Warning: Atom names in each residue should be unique.
     (Same-name atoms are handled by using the first
      occurrence and by ignoring the rest.
      Frequently duplicate atom names stem from alternate
      conformations in the PDB file.)
Unknown residue: MG number: 154 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Created a new atom named: H within residue: .R<NCYS 1>
Creating new UNIT for residue: MG sequence: 155
Created a new atom named: MG within residue: .R<MG 155>
  total atoms in file: 2381
  Leap added 3 missing atoms according to residue templates:
       3 H / lone pairs
  The file contained 2 atoms not in residue templates
> saveAmberParm mol wt1mg_dry.parm7 wt1mg_dry.rst
Checking Unit.
FATAL: Atom .R<NCYS 1>.A<H 14> does not have a type.
FATAL: Atom .R<MG 155>.A<MG 1> does not have a type.
Failed to generate parameters
Parameter file was not saved.
I don't know how to solve such problem. Please give me some suggestion.
Thank you!

School of Life Science and Technology
Xi'an Jiaotong University
Mailbox 2046 No.28 Xianning West Road
Xi'an, Shaanxi, 710049, P.R.China
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Received on Thu Apr 22 2010 - 19:00:02 PDT
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