RE: AMBER: (no subject)

From: Ross Walker <>
Date: Wed, 14 Jul 2004 11:33:38 -0700

Dear Anshul,

> I am going through the plastocynin tutorial. Can you tell me
> how I can use
> GAFF of antechamber for this purpose, since i could not
> figure out how to
> use the resp charges generated by RED as there is no relevent
> file type
> which can be used.

What you need to do is fire up xleap with the force field you want to use
for the main part of your protein, e.g for ff99:

xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99

Then you should load the parameters for the GAFF force field, note these
have lowercase atom names so should not cause a clash with the FF99

You then need to create a new residue for the molecule that you don't have
parameters for and assign the relevant GAFF atom types and enter the charges
that you calculated. You should then be able to load your pdb file for your
protein + extra residue and all of the residues should be successfully
recognised. You can then save a prmtop and inpcrd file that will contain a
mixture of the FF99 params (for the protein) and GAFF params for your extra
residue. Alternatively you could get antechamber to assign the atoms types
for you, although I think it is often better, and less error prone, to do
these things by hand. See the manual for an example on using Antechamber.
This will allow you to create a prep file that you can load into xleap
before you load your pdb file. - note you will still need to use
loadamberparams gaff.dat to load the GAFF force field params into leap.

> another thing i would like to ask is that what do you mean by
> saying "be
> aware of exactly what you are doing and what the implications are."

Exactly that, think about what you are doing and check the atom types etc
carefully. Also be aware that you will be mixing two force fields. Now,
although these two force fields use the same equation and are sufficiently
similar that they can be used together just be aware that there may be
slight imbalances that 'could' lead to artificial results. Just a warning,
that is all...
> what i want to do is that i want to add atrazine molecule to
> a protein at
> lysine residues. for this i generated resp charges for
> atrazine attached
> to lysine and now i would like to replace the lysine residues in the
> protein by this unit and do molecular dynamics of the system
> to check the
> effect of such substitution. Is my approach right or not?

Yes although you may encounter problems if your atrazine is directly bound
to the lysine, in this case you will end up with bonds, angles and dihedrals
that cross the FF99 to GAFF boundary. There are no parameters for this...
You will need to either create some, modify some existing parameters or
locate some that have been published.

> and will it be
> fine by getting parameters from antechamber suit (GAFF) for
> this purpose?

Yes BUT you will have to deal with the boundary between atazine and lysine

What you may want to do is create a whole new residue like LYA or something
that includes the LYSINE and the ATRAZINE (if they are bound) and use this
in place of the lysines in your protein.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Wed Jul 14 2004 - 19:53:00 PDT
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