AMBER Archive (2006)

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

From: Zhihong Yu (
Date: Sat Jun 03 2006 - 02:00:23 CDT

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

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