AMBER Archive (2006)

Subject: Re: AMBER: GLYCAM and ff98 atom-types]

From: Austin B. Yongye (ayongye_at_chem.uga.edu)
Date: Thu Nov 16 2006 - 13:53:03 CST

> I am trying to simulate a system with carbohydrates and a protein. The
> plan is to use GLYCAM and AMBER ff98. My question is how can I load the
> two force-fields in Leap?

Source both leaprc.glycam04 and leaprc.ff98 in your leap command file, or
in t/xleap.

> Do I need to edit one of the leaprc files to include either glycam in
(or > the other way around)?

You could, by adding all the input from one file to the other, making sure
there are no duplicate entries. Then you can source only this single file.
However, I would be strongly inclined to source both files separately.

> Also, I am concerned about the difference in atom types that occur in
the > two leaprc files.
> leaprc.glycam04
> { "CG" "C" "sp3" }
> { "CY" "C" "sp3" }
> leaprc.ff98
> { "CG" "C" "sp2" }
> { "CY" "C" "sp2" }

CY and CG atom types are not present in parm98.dat. But CY is in
parm99.dat to represent the nitrile C atom. Since CG and CY are specific
to glycam up till parm99.dat, FOR NOW, you can safely change the
hybridisations to sp3.
austin-

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