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