Hi.
I do not remember what the problem was, but why you load the *.lib and the
*.prp files. I normally use *.prp and *.frcmod. Both the *.lib and the
*.prp do essentially the same. They tell tleap the atoms of your ligand,
the name for each atom and what's the atom type in the forcefield. So as
long as your pdb for the complex has the ligand with the right atom names,
you can do only the second process. What I normally do is use the pdb file
created by antechamber when you create the *.prp and *.frcmod from the
gaussian file, manually dock that pdb of the ligand into the active site of
my enzyme (using pymol for example), save the pdb with the new coordinates,
copy and paste it in the enzyme pdb file (replacing if necessary the
previous ligand), and the use that file for running the tLeap. That way you
avoid problems with the name of the atoms of the ligand.
Hope it helps
2015-10-15 22:07 GMT+02:00 MarcZhang <progress0935zhang.gmail.com>:
> Dear Emilio Lence
>
>
>
> Thanks a lot for your reply
>
>
>
> Here is my instructions to tleap for ligand parameter generation:
>
>
>
> set default PBradii mbondi2
>
> source leaprc.ff99SB
>
> source leaprc.gaff
>
> BP1=loadmol2 BPH-TTR_Ligand1_resp.mol2
>
> loadamberparams BPH-TTR_Ligand1_resp.frcmod
>
> loadamberprep BPH-TTR_Ligand1_resp.prep
>
> check BP1
>
> saveoff BP1 BP1.lib
>
> saveamberparm BP1 BPH-TTR_BP1_resp_nW.prmtop BPH-TTR_BP1_resp_nW.inpcrd
>
> quit
>
>
>
> Here is the instructions to tleap for complex parameter generation:
>
>
>
> set default PBradii mbondi2
>
> source leaprc.ff99SB
>
> source leaprc.gaff
>
> loadamberparams frcmod.ionsjc_tip3p
>
> loadamberparams BPH-TTR_Ligand1_resp.frcmod
>
> loadamberprep BPH-TTR_Ligand1_resp.prep
>
> loadoff BP1.lib
>
> check
>
> Complex=loadpdb BPH-TTR_Complex.pdb
>
> saveamberparm Complex BPH-TTR_Complex_nW.prmtop BPH-TTR_Complex_nW.inpcrd
>
> savepdb Complex BPH-TTR_Complex_nW.pdb
>
> solvateoct Complex TIP3PBOX 10.0
>
> charge Complex
>
> addions Complex Na+ 0
>
> addions Complex Cl- 0
>
> charge Complex
>
> check Complex
>
> saveamberparm Complex BPH-TTR_Complex_Solvated.prmtop
> BPH-TTR_Complex_Solvated.inpcrd
>
> savepdb Complex BPH-TTR_Complex_Solvated.pdb
>
> quit
>
>
>
> Can you figure out where the issue it? Please inform me if you require more
> information.
>
>
>
> Thanks very much!
>
>
>
> Cheers
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Emilio Lence Quintana
Organic Chemistry Department-CIQUS
University of Santiago de Compostela
15782 Santiago de Compostela, Spain
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Received on Sat Oct 17 2015 - 08:00:03 PDT
