> On Apr 20, 2015, at 6:58 AM, neha chaudhary <nehachaudhary769.gmail.com> wrote:
>
> Hello Sir,
>
> I have simulated a protein-ligand structure in gromacs, now I am want to
> convert the output .pdb (protein-ligand) file into .prmtop using amber14.
> Firstly I was using antechamber for this purpose but it ended with
> segmentation fault. Then I tried tleap and xleap also but it also failed.
> Can you help me with this conversion of .pdb file into .prmtop. Suggest me
> any other software suitable for this conversion.
Your question lacks any specific details about what you did. To avoid making us guess, provide specific details of what you did, what you tried, and what error messages you received (be explicit -- give us exact input, output, and commands; often when people make mistakes, they did something different than what they thought they did or what they tried to do).
My best guess as to what you did was to take your entire protein-ligand system, turn it into a PDB file, and give the whole thing to antechamber. This is not the right thing to do. What you need to do is extract *only* the ligand in a separate PDB file and use antechamber to generate a residue library file (e.g., a mol2 file) for your ligand. Use parmchk to generate a frcmod file using gaff, then load the PDB file, the mol2 file, and the frcmod file into tleap in order to save a topology file.
Above is the basic outline of what needs to be done, but there is no way that anybody can (or should) explain how to use these programs better in an email post than we do in the tutorials that are available: see http://ambermd.org/tutorials/ <http://ambermd.org/tutorials/> for a list of available tutorials. In particular, look at tutorial B4 with regards to simulating an organic ligand.
For future questions, make sure you reduce the problem as much as you can (i.e., narrow it down to only a small number of steps needed to reproduce the problem), and provide all of the relevant input and output exactly as you saw it so we know exactly what you did and what happened.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Apr 20 2015 - 06:30:03 PDT
