On Wed, 2013-12-04 at 18:30 +0330, Saeed Nasiri wrote:
> 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*
This tells me that your residue name is 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*
Here you save the residue BMI to "bmi.lib". Now when you load the
bmi.lib OFF file, it will add "BMI" as an available residue (unit) in
tleap.
> 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
This tells me that the residue names in "ionic.pdb" is "bmi". However,
the residue you saved in the bmi.lib file is "BMI". Residue and atom
names are case-sensitive, and you must make sure that the residue names
in your PDB file are *exactly* the same as the residue name you saved in
the library template file. An easy way of doing this in your case is to
change "bmi" to "BMI" in your ionic.pdb file everywhere that it occurs.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Dec 04 2013 - 07:30:03 PST
