> On Feb 16, 2015, at 7:44 AM, Fatemeh Sadat Alavi <f_alavi.sbu.ac.ir> wrote:
>
>
>
>
> I am going to do Amber calculation for molecular simulation of my system.
> My system includes heme and protein.I created required file for ligand
> containing lig.frcmod, lig.prmtop, lig.inpcrd with respect to output from
> ESP calculation by Gaussian software,well.
> I made these files fro protein by Amber software,too.
> For next step, I should build complex.While atom labels in the pdb file for
> ligand are the same labels used in my generated mol2 file,I have error about
> atom type of ligand.
> I attached lig.mol2 and complex.pdb and errorscript.txt to this mail.
In your leap script, you put the command:
LIG = loadmol2 LIG.mol2
This takes the residue defined in LIG.mol2 and assigns it to the residue unit “LIG”. However, in your PDB file, you have the residue name HEM, so the names don’t match in tleap and your PDB file.
You need to assign the unit in LIG.mol2 to the residue named HEM instead of LIG:
HEM = loadmol2 LIG.mol2
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Feb 16 2015 - 06:00:04 PST
