Dear Amber Users and Developers,
Following the e-mails from Professors Hannes Loeffler and David Case, we
compared GAFF and GAFF2.
We noticed that gaff2.dat introduces 12 new atomtypes (cs, n+, n7, n8, n9,
ns, nt, nu, nv, nx, ny, nz), which is good. For instance, "cs" is a Sp2 C
in C=S, replacing "c ". However the hybridizations of the new atomtypes are
not included in the leaprc.gaff2 file…
Moreover, we'd like to point out that for a simple thiourea, which includes
the "cs" atomtype, when we generate a frcmod file, this "cs" atom type is
listed in the "NONBON" section of the frcmod file. Indeed, in gaff2.dat,
the "cs" atomtype is listed only under the "MASS" and "DIHE" sections - no "
NONBON" parameters! This leads to the *tleap *warning "No mass defined for
non-bond atom type: cs - skipping" and we had to include the "MASS"
information in the frcmod file to avoid this issue.
The lack of bond and angle parameters for "cs" in gaff2.dat is explained in
the frcmod file, as *parmchk2* applies the bond and angle parameters of "c
".
Still, on the matter of bond and angle parameters, we also noticed that for
several bonds and angles, although the equilibrium bonds/angles did not
change or changed a little, the force constants are quite different – this
can only mean that either the equations given in the GAFF original paper
changed or that some of the empirical values were updated. This will be
clarified in the GAFF2 paper, correct? When can we expect it?
Best wishes,
Many thanks,
Igor
Igor Marques, PhD Student
MSc in Pharmaceutical Biomedicine
BSc in Biomedical Sciences
Molecular Modeling Group – University of
Aveiro
http://molecular-modeling.dq.ua.pt/
Mobile phone: +351 918 567 294
Landline: +351 234 247 254
Through PBX: +351 234 370 200 (ext. 22160)
Universidade de Aveiro
Campus Universitario de Santiago
Agra do Crasto – Edificio 30
3810-193 Aveiro - Portugal
On Thu, May 19, 2016 at 1:06 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Thu, May 19, 2016, Hannes Loeffler wrote:
> >
> > I suppose this should be painfully obvious but just to confirm how to
> > set up a system with GAFF2.
> >
> > antechamber -at gaff2 which triggers atomtype -p gaff2
> > parmchk2 -s gaff2
> >
> > and finally, in leap:
> >
> > source leaprc.gaff2
>
> Above is correct....dac
>
>
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Received on Fri Jun 03 2016 - 13:00:02 PDT
