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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Received on Thu Apr 15 2004 - 07:53:00 PDT
