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

From: Navnit Kumar Mishra <>
Date: Mon, 05 Jun 2006 10:08:12 +0200

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,

Zhihong Yu wrote:

> Dear All,
> First of all, thanks Dr. Case and Martin for your answers to my last
> questions!
> Now I've extracted a ligand from crystal structure pdb file, and then
> modified the atom types and bond types in SYBYL, the generated mol2
> file (called it as mol2-A file) was submitted to Gaussian03 to get
> resp charge, then I generated another mol2 (called it as mol2-B file)
> file with the resp charge and gaff atom type using antechamber, then I
> read this mol2 file into xleap and generated corresponding prmtop and
> inpcrd files just as Ross Walker's did in his beginer tutorial 5. Here
> I have some questions:
> 1: The Cartesian coordinates in mol2-A and mol2-B files are different,
> in mol2-A these coordinates are same as they are in pdb file, but in
> mol2-B it looks like these coordinates were taken from the "Atomic
> Center" in "Electrostatic Properties Using The SCF Density" part in
> the gaussian output file. These difference would affect the final
> parameters in prmtop and inpcrd for MD or not ? should I change these
> coordinates in mol2-B with corresponding values in pdb file?
> 2: I get the resp charges only from HF/6-31G* single point calculation
> in Gaussion03 , someone use single point calculation while someone use
> optimized result in literatures, so I wondered whether geometry
> optimization is necessary or not?
> 3: I want perform a MD on the complex system while not just on the
> recptor or ligand, then after I get thd prmtop and inpcrd file for the
> ligand, how can I use them in my prmtop and inpcrd generation
> procedure for the complex system ?
> Any adivce will be appreciated, thanks in advance!
> sincerely, Zhihong
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jun 07 2006 - 06:07:08 PDT
Custom Search