[AMBER] Fwd: Atom type assignment using GAFF

From: abc def <biotechabc.gmail.com>
Date: Fri, 12 Nov 2010 20:25:37 +0530

Hi all,

Can anyone please tell me how to do this? Or can let me know from where I
can read about this? Please.

Thanks in advance,

B.E. Biotechnology
NSIT, Delhi

---------- Forwarded message ----------
From: abc def <biotechabc.gmail.com>
Date: Fri, Nov 12, 2010 at 7:32 AM
Subject: Atom type assignment using GAFF
To: amber.ambermd.org


Thanks for replying to my earlier queries Now there is one more problem that
I am facing.

I used gaff parameters for my ligand molecule. But after loading the prepin
and frcmod file, when I loaded pdb file, I got the following error

+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-N2-C1-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes

I found out that +NH2=C-- the atoms in this group are not properly
assigned. N is assigned sp3 (nh) where it should have been sp2
hybridized and the type of C here couldnt be recognized. How should I change
the atom type of N and should assign an atom type to C here? And what atom
type should I assign to N and C?

>From the paper on gaff force field parameter develpment, I felt that the
atom type for N should be 'na' and that of C should be 'ca'. But I am not
sure and want to confirm the same?

I am new to amber and dont know how to change the atom types and when
changing atom type and assigning new atom types, what all other changes I
need to make in the other files (say frcmod)?

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Received on Fri Nov 12 2010 - 07:00:07 PST
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