Dear nalini,
You need to create a PDB for your bioinorganic complex.
See for instance: http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#8
if you decide to use RED Server Dev. no need to create a P2N file;
just provide the PDB file. You also need to define the total charge
and the spin multiplicity of your complex.
regards, Francois
> I have been working on the MD simulation of a Dimeric protein containing
> Zinc ions. I was trying to simulate its monomer which contains single zinc
> ion. I have gone through TUTORIAL A1 Old: Building your own Custom
> Residues ,described in AMBER, but after creating .lib file I am confuse
> regarding specifying the atom types and charges. I was working on RED
> server but I am still not getting how to get QM file for my ion bounded
> residues.
> ---------- Forwarded message ----------
> From: <amber-owner.ambermd.org>
> Date: 15-Feb-2014 8:35 AM
> Subject:
> To: <nalinichauhan.05.gmail.com>
> Cc:
>
> Message rejected by filter rule match
>
>
>
> ---------- Forwarded message ----------
> From: nalini chauhan <nalinichauhan.05.gmail.com>
> To: amber.ambermd.org
> Cc:
> Date: Sat, 15 Feb 2014 08:35:14 +0530
> Subject:
> Respected Sir,
>
> I have been working on the MD simulation of a Dimeric protein
> containing Zinc
> ions. I was trying to simulate its monomer which contains single zinc ion.
> I have gone through TUTORIAL A1 Old: Building your own Custom Residues
> ,described
> in AMBER, but after creating .lib file I am confuse regarding specifying
> the atom types and charges. I was working on RED server but I am still not
> getting how to get QM file for my ion bounded residues.
>
> It will be great if you could just tell me where am I wrong or what
> procedure to follow.
>
> Thanks.
>
> Regards,
>
> Nalini
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 16 2014 - 04:00:02 PST
