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 - 10:30:06 PST
