Hi Dr. Case,
> Please use the "list" command in tleap (before issuing the loadPdb command)
> to make sure you have an unit named MG, and that it contains what you think
> it should.
>
> Then, if you get error messages when you issue the loadPdb command, read
> them
> very carefully, and try to figure out how to understand what they are
> saying.
I find the solution, which probably is correct...
I use the script of ions94.cmd about Mg ion, and modify all MG2 to be
MG, then save it in ions94.cmd, use the command tleap -f ions94.cmd.
After checking ions94.lib and xleap by "list", there is a unit MG, and
it helps xleap to recognize magnisum ions whose symbol is MG in the
pdb, and generate prmtop and inpcrd files. I also can use this unit MG
to add Mg2+ ions to neutralize charges of the structure (that is a
test...), as what MG2 can do in the xleap.
======this is the modified version of script of Mg2+ ion in ions94.cmd========
i = createAtom MG MG 2.0
set i element Mg
set i position { 0 0 0 }
r = createResidue MG
add r i
MG = createUnit MG
add MG r
saveOff MG ./ions94.lib
==================================
=====This is the test result ====================
(ps: MG_test.pdb only contains two Mg2+ ions and use the symbol MG in pdb)
> mg=loadpdb "MG_test.pdb"
Loading PDB file: ./MG_test.pdb
Enter zPdbReadScan from call depth 0.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
(Residue 0: MG, Terminal/beginning, was not found in name map.)
(Residue 1: MG, Terminal/last, was not found in name map.)
Starting new chain with MG
total atoms in file: 2
> saveamberparm mg test_mg.prmtop test_mg.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: 4.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 0 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(no restraints)
=============================================
Is it right so I can apply the same way to treat Cl and other metal
ions available in ions94.lib? Thank you and Junmei very much for your
suggestions and guidance so far.
Sincerely,
Crystal
>
> If you still can't see how to proceed, try to make a small sample pdf file
> that illustrates the problem, and post it, along with the *exact* commands
> you are using.
>
> ...good luck...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 18 2011 - 14:30:03 PST
