AMBER Archive (2006)

Subject: Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system?

From: Zhihong Yu (
Date: Mon Jun 05 2006 - 03:57:44 CDT

>Hello Zhihong;
>In your complex the coordinate look different but if you see the
>internal coordinates it shouldn't be changed, in prep file there is
>information of internal coordinate (Z-matrix), charge, and atom types..
>So, when you load any pdb file with residue name similar to your loaded
>prep file, the leap matched it and defined according to your prep file.
>You can also use your starting coordinate to make your ligand topology
>and parmeter file, becoz by antechamber you have prepared prep file, you
>only need to load this prep file in leap.
>In the same way you can prepare complex topology and coordinate from
>your crystal struc can doit in this way
>source leaprc.ff03 (any force field)
>loadamberprep ligand.prep
>PDB=loadpdb Your.pdb
>saveamberparm pdb.inpcrd
>you should put the residue name for ligand in your pdb file similar to
>your residue name in ligand prep file.
>if your interaction doesn't affect due to some geometrical change than
>point charge calculation is ok. But I think its good to first optimized
>your system to freaz the heavy atom and then you reoptimize the
>structure by point charge calculation. its only my view, it also depends
>on several properties.
>I hope it will help you,

Thanks Navnit for your kindness!

In fact, I think the ligand's conformation extracted from complex is so called "bioactive conformation", so resp charges from this conformation maybe more preferable than that only from optimzed conformation in gas phase. while because the hydrogens are added arbitrarily by certain program, as you mentioned that optimization freezed heavy atoms maybe a good idea.

In addition, besides the ligand there are many cofactors in my complex system such as FAD, Mg2+ etc, now I can prepare organic small molecules' parameters for leap, but how can I generate the prep file for metal ions such as Mg2+?

Thanks in advance!


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