[gmx-users] Please help me with ACPYPI

TRANG NGUYEN tructrang27 at gmail.com
Mon Mar 1 05:44:55 CET 2010

Dear All,

I would like to ask for your help to my problem dealing with making topology
file for ligand with OPLS-AA forcefield by following

Now, let me show you my steps:
- Getting my ligand.pdb file from PDB
- Adding all hydrogen by PRODRG2.5 Server with GROMOS 87 forcefield, full
charges, no EM, full chirality
- Using antechamber to convert ligand.pdb to ligand_bcc.pdb
(antechamber -i ligand.pdb -fi pdb -o ligand_bcc.pdb -fo pdb -c bcc)
- Running ACPYPI (acpypi -i ligand_bcc.pdb), then obtaining folder
ligand_bcc.acpypi, including my wanted file: ligand_bcc_GMX_OPLS.itp.

However, some problems occured:
    17 opls_x     1   MOL   O24   17    -0.447600      0.00000 ; qtot
-0.186  x
    22 opls_x     1   MOL    C4   22    -0.147400      0.00000 ; qtot
-0.168  x
It seems that OPLS-AA forcefield does not recognize what Amber forcefield
have assigned for this atomtype/bondtype. Then, it stopped me there from
running the next steps in order to perform modeling dynamics simulation of
protein-ligand complex in Gromacs with OPLS-AA forcefield.

Could you please help me to solve this problem?

I really hope to hear from you soon!

Thanks in advances!
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