Dear Dr David A Case
Thanks for your quick replying. I did all things that you told. I could
save parameters for a single bmi ion but not in the simulation box? I read
something about define residue for new molecules in amber, but I don't know
I should use addAtomtype commands (was not work for me) in tleap or create
.prepin file or .off file.
I read these in the following links.
Your Sincerely
Saeed Nasiri
http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-nonstandard/
http://ambermd.org/tutorials/advanced/tutorial8/loop1.htm
============================================================
*tleap*
-I: Adding /home/nasiri/amber12/dat/leap/prep to search path.
-I: Adding /home/nasiri/amber12/dat/leap/lib to search path.
-I: Adding /home/nasiri/amber12/dat/leap/parm to search path.
-I: Adding /home/nasiri/amber12/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
*> source leaprc.gaff*
----- Source: /home/nasiri/amber12/dat/leap/cmd/leaprc.gaff
----- Source of /home/nasiri/amber12/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/nasiri/amber12/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.5, January 2013)
*> BMI = loadmol2 bmi.mol2*
Loading Mol2 file: ./bmi.mol2
Reading MOLECULE named bmi
*> check BMI*
Checking 'BMI'....
WARNING: The unperturbed charge of the unit: 0.999998 is not zero.
Checking parameters for unit 'BMI'.
Checking for bond parameters.
Checking for angle parameters.
Could not find angle parameter: na - cc - na
There are missing parameters.
check: Warnings: 1
Unit is OK.
*> loadamberparams frcmod.bmi*
Loading parameters: ./frcmod.bmi
Reading force field modification type file (frcmod)
Reading title:
remark goes here
*> saveoff BMI bmi.lib*
Creating bmi.lib
Building topology.
Building atom parameters.
*> saveamberparm BMI bmi.top bmi.crd*
Checking Unit.
WARNING: The unperturbed charge of the unit: 0.999998 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 5 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
bmi 1
)
(no restraints)
*> ionicbox = loadPdb ionic.pdb*
Loading PDB file: ./ionic.pdb
Unknown residue: bmi number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: bmi sequence: 1
Created a new atom named: C1 within residue: .R<bmi 1>
Created a new atom named: N2 within residue: .R<bmi 1>
Created a new atom named: N3 within residue: .R<bmi 1>
Created a new atom named: C4 within residue: .R<bmi 1>
Created a new atom named: C5 within residue: .R<bmi 1>
Created a new atom named: C6 within residue: .R<bmi 1>
Created a new atom named: C7 within residue: .R<bmi 1>
Created a new atom named: C8 within residue: .R<bmi 1>
Created a new atom named: C9 within residue: .R<bmi 1>
Created a new atom named: C10 within residue: .R<bmi 1>
Created a new atom named: H11 within residue: .R<bmi 1>
Created a new atom named: H12 within residue: .R<bmi 1>
Created a new atom named: H13 within residue: .R<bmi 1>
Created a new atom named: H14 within residue: .R<bmi 1>
Created a new atom named: H15 within residue: .R<bmi 1>
Created a new atom named: H16 within residue: .R<bmi 1>
Created a new atom named: H17 within residue: .R<bmi 1>
Created a new atom named: H18 within residue: .R<bmi 1>
Created a new atom named: H19 within residue: .R<bmi 1>
Created a new atom named: H20 within residue: .R<bmi 1>
Created a new atom named: H21 within residue: .R<bmi 1>
Created a new atom named: H22 within residue: .R<bmi 1>
Created a new atom named: H23 within residue: .R<bmi 1>
Created a new atom named: H24 within residue: .R<bmi 1>
Created a new atom named: H25 within residue: .R<bmi 1>
total atoms in file: 25
*The file contained 25 atoms not in residue templates*
> setbox ionicbox centers
Box dimensions: 4.274000 5.635000 9.170000
*> saveAmberParm ionicbox ionicbox.prmtop ionicbox.inpcrd*
Checking Unit.
FATAL: Atom .R<bmi 1>.A<C1 1> does not have a type.
FATAL: Atom .R<bmi 1>.A<N2 2> does not have a type.
FATAL: Atom .R<bmi 1>.A<N3 3> does not have a type.
FATAL: Atom .R<bmi 1>.A<C4 4> does not have a type.
FATAL: Atom .R<bmi 1>.A<C5 5> does not have a type.
FATAL: Atom .R<bmi 1>.A<C6 6> does not have a type.
FATAL: Atom .R<bmi 1>.A<C7 7> does not have a type.
FATAL: Atom .R<bmi 1>.A<C8 8> does not have a type.
FATAL: Atom .R<bmi 1>.A<C9 9> does not have a type.
FATAL: Atom .R<bmi 1>.A<C10 10> does not have a type.
FATAL: Atom .R<bmi 1>.A<H11 11> does not have a type.
FATAL: Atom .R<bmi 1>.A<H12 12> does not have a type.
FATAL: Atom .R<bmi 1>.A<H13 13> does not have a type.
FATAL: Atom .R<bmi 1>.A<H14 14> does not have a type.
FATAL: Atom .R<bmi 1>.A<H15 15> does not have a type.
FATAL: Atom .R<bmi 1>.A<H16 16> does not have a type.
FATAL: Atom .R<bmi 1>.A<H17 17> does not have a type.
FATAL: Atom .R<bmi 1>.A<H18 18> does not have a type.
FATAL: Atom .R<bmi 1>.A<H19 19> does not have a type.
FATAL: Atom .R<bmi 1>.A<H20 20> does not have a type.
FATAL: Atom .R<bmi 1>.A<H21 21> does not have a type.
FATAL: Atom .R<bmi 1>.A<H22 22> does not have a type.
FATAL: Atom .R<bmi 1>.A<H23 23> does not have a type.
FATAL: Atom .R<bmi 1>.A<H24 24> does not have a type.
FATAL: Atom .R<bmi 1>.A<H25 25> does not have a type.
Failed to generate parameters
Parameter file was not saved.
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Received on Wed Dec 04 2013 - 07:30:02 PST
