Hi,
Thanks for reply. I will go through it.
*Thanks & Regards,*
*Yogeeshwar Ajjugal*
On Tue, Feb 16, 2016 at 11:52 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Feb 16, 2016, Yogeeshwar Ajjugal wrote:
>
> >
> > Iam trying to study DNA-protein interaction with Amber12
> > (ff12SB). The crystal structure contains single MG atom with net charge
> > zero.However i was unable to generate prmtop and prmcrd files. its
> showing
> > MG atom type not found.I will be very much thankful, if you kindly help
> me
> > regarding this.
> >
> > *Note: I gone through the previous threads regarding this issue and
> taken
> > into consideration, i changed atom type MG to MG2 in pdb file i can able
> to
> > generate prmtop and crd files by using ff99SB but here i want to use
> > ff12SB.*
>
> It is generally necessary to load a particular ion forcefield in addition
> to
> general ff files like ff12SB or ff14SB. This is because ion parameters are
> strongly coupled to the water model you are using.
>
> You likely want to load something like frcmod.ionslrcm_cm_tip3p, which is
> the
> "compromise" divalent ion parameters for tip3p water. See Section 3.10 in
> the
> Amber 2015 Reference Manual for a full discussion of this.
>
> ....dac
>
>
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Received on Tue Feb 16 2016 - 21:30:04 PST
