Dear all,
I was trying to get the prmtop file and inpcrd file by using xleap
(adding counter-ion, adding water box). I was using the parm99 additive
force field. And the system I am studying is protein plus DNA (regular
amino acid and DNA bases). But in the leap.log file, I found something
like this:
Matching PDB residue names to LEaP variables.
Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA.
(Residue 1: GLU, Nonterminal, was not found in name map.)
(Residue 2: TRP, Nonterminal, was not found in name map.)
(Residue 3: SER, Nonterminal, was not found in name map.)
(Residue 4: GLY, Nonterminal, was not found in name map.)
....
....
> saveamberparm model2 1mj2_K44Q_wat.prmtop 1mj2_K44Q_wat.incrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for NB-C-CB-CB
atoms are: N7 C6 C5 C4
** Warning: No sp2 improper torsion term for N*-CB-CB-NC
atoms are: N9 C5 C4 N3
** Warning: No sp2 improper torsion term for NB-C-CB-CB
atoms are: N7 C6 C5 C4
** Warning: No sp2 improper torsion term for N*-CB-CB-NC
atoms are: N9 C5 C4 N3
** Warning: No sp2 improper torsion term for NB-C-CB-CB
atoms are: N7 C6 C5 C4
....
So my question is: (1) in the first part of the log file, why are those
residues were not found in name map? Would it matter? (2) in the second
part of the log file, there are some warning message about missing
improper torsion term. Why are they missing?
Another question is about water. If I want to include water molecules in
the crystal structure, what should I do? Do I need to change the name of
each molecule and add "TER" after that?
Thanks a lot for your kind help!
Best,
Jeny
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Received on Mon Jun 28 2004 - 15:53:01 PDT
