Dear Amber users,
I am new in Amber and rather confused.
Lets say i want to simulate smth very simple - benzonitrile molecule
(simplest molecule with cg atomtype)
I make gaussian calculation for resp charges, create .mol2 file with
antechamber, generate .frcmod file with prmchk, combine them in leap and
got .top and .crd files
Then I use amb2gmx.pl tool and convert .top and .crd into gromacs
topology file. This file contain lines
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon
ca ca 0.0000 0.0000 A 3.39967e-01 3.59824e-01
n1 n1 0.0000 0.0000 A 3.25000e-01 7.11280e-01
ha ha 0.0000 0.0000 A 2.59964e-01 6.27600e-02
cg cg 0.0000 0.0000 A 3.39967e-01 _/*8.78640e-01*/_
that looked perfect before i opened file from
http://virtualchemistry.org/molecule.php?filename=benzonitrile.zmat
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon
cg cg 0.0000 0.0000 A 3.39967e-01 _/*3.59824e-01*/_
ha ha 0.0000 0.0000 A 2.59964e-01 6.27600e-02
ca ca 0.0000 0.0000 A 3.39967e-01 3.59824e-01
n1 n1 0.0000 0.0000 A 3.25000e-01 7.11280e-01
I tried to google these values and found that 8.78640e-01 corresponds in
few forcefields (for example in
http://wwwuser.gwdg.de/~ckutzne/git-gromacs-46-density/share/top/amber03.ff/ffnonbonded.itp)
to Oxygen atom. Does this mean that amb2gmx.pl is doing smth wrong, or
mistake is somewhere before, or data on virtualchemistry is incorrect?
Thanks in advance,
Dmitriy.
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Received on Wed Aug 12 2015 - 15:30:03 PDT
