Pranabesh,
the prp (=prepi) file contains the definition of the residue and the
associated atoms, i.e. a residue MNG with a single atom named MN bearing
an atomic charge of +2.
The dat (=frcmod) file contains the parameters, i.e. the element mass
and the two non-bonded parameters for the vdW potential.
When you set up your simulation via leap, you have to load the
parameters prior to loading your protein system. Have a look into the
Amber21 manual, section 3 (p. 37) for more on this.
Place the loading of your special Mn parameters after loading the
standard ones:
[...]
# Load Mn parameters
loadamberparams metals.dat
loadamberprep metals.prp
# Load protein system with Mn ions
[...]
In your input pdb file, ensure that your Mn ions have the same atom and
residue name as defined in the prepi file, i.e. MNG and MN, respectively.
If this does not work, try to setup a test system with only one Mn ion
in order to isolate potential input errors, and work on from that.
(If you are new to Amber, be sure that you have a basic knowledge of the
theory and the workflow; the Amber website provides great tutorials!)
Hope that helps.
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 01/05/2022 12:49 PM, Pranabesh Mandal (PhD, Bioinformatics
August-2019) wrote:
> Dear members,
> I am trying to perform a molecular dynamics simulation of a protein with
> four Mn2+ present in the binding site. The non bonded parameters are
> downloaded from the AMBER parameter database (.dat and .prp file).
>
> I am new to amber and I don't know how to use those files for multiple
> non-bonded Mn2+ ions and perform the md simulation in amber.
>
> I appreciate all help and look forward to any responses from you.
>
>
> Thank you
> Pranabesh Mandal
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Received on Wed Jan 05 2022 - 05:00:02 PST
