AMBER Archive (2004)

Subject: AMBER: Problem in loading a PDB file in Leap - Please help me

From: Mike (amber_list_at_speedpost.net)
Date: Thu Apr 15 2004 - 01:25:07 CDT

Hi AMBER users,

I have a problem in running tleap .. I tried to load a pdb file with Mg
ion on it.

I could not create .top and .crd file with mg ion on it.

Actually, there is an MG ion in ions94.lib and i don't know why AMBER is
not recognizing it.

I have given the snapshot of the errors and i have also attached my .pdb
file with this thread.

I would greatly appreciate if you could give a solution for this problem.

Thanks in advance.
Mike

****************************************************************

> mg_last_mod = loadpdb mg_last_mod.pdb
Loading PDB file: ./mg_last_mod.pdb
 (starting new molecule for chain B)
 (starting new molecule for chain 4)
Unknown residue: number: 294 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Created a new atom named: P within residue: .R<DA5 1>
Created a new atom named: O1P within residue: .R<DA5 1>
Created a new atom named: O2P within residue: .R<DA5 1>
Created a new atom named: P within residue: .R<DA5 148>
Created a new atom named: O1P within residue: .R<DA5 148>
Created a new atom named: O2P within residue: .R<DA5 148>
Creating new UNIT for residue: sequence: 295
Created a new atom named: MG M within residue: .R< 295>
  total atoms in file: 9349
  Leap added 4 missing atoms according to residue templates:
       4 H / lone pairs
  The file contained 7 atoms not in residue templates

> saveamberparm mg_last_mod mg_last_mod.prmtop mg_last_mod.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -292.000000 is not zero.
FATAL: Atom .R<DA5 1>.A<P 31> does not have a type.
FATAL: Atom .R<DA5 1>.A<O1P 32> does not have a type.
FATAL: Atom .R<DA5 1>.A<O2P 33> does not have a type.
FATAL: Atom .R<DA5 148>.A<P 31> does not have a type.
FATAL: Atom .R<DA5 148>.A<O1P 32> does not have a type.
FATAL: Atom .R<DA5 148>.A<O2P 33> does not have a type.
FATAL: Atom .R< 295>.A<MG M 1> does not have a type.
Failed to generate parameters
Parameter file was not saved. 

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