On Fri, Jan 30, 2015 at 2:22 PM, Ilyas Yildirim <iy222.cam.ac.uk> wrote:
> Hi Carlos,
>
> It seems that the RADII for the new atom types are set to 2.2 Ang while
> the old values are 1.7 Ang and this 2.2 Ang seems to be causing the
> problem. Maybe I need to specify these atom types somewhere in the code? It
> seems that unitio.c file, line # 6149 has Carbon atom radii set to 2.2. The
> new atom types I have are named as C1, C2, C3, and C4. Is there any simple
> way to make sure the correct radii are used for the new atom types without
> changing the code? Thanks.
>
This was something I fixed a while ago. I will preface this with the
statement that 1.7 angstroms is the correct value. C1, C2, and C3 were, in
the early days of the Amber force field, reserved for UA force fields where
the number indicated how many hydrogens were folded into that carbon. So
the C1/C2/C3 atom types were assumed to have a larger radius (2.2 A) with a
larger mass (13.02 amu). Unfortunately, Amber has a hard-coded limit of 2
characters per atom type, and the C1, C2, and C3 atom types were hijacked
for use in the AA force fields (as there haven't been any UA Amber force
fields developed in some time), but the LEaP code was never updated for
this. I fixed this in November, 2013, so the first version of leap to
have this fix was Amber 14.
Long story short -- don't use leap 12 :). Scott -- is the 2.2 A the root
cause of the issue?
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 30 2015 - 12:00:02 PST
