friendli wrote:
Thank you Justin.
Can you tell me how i can find the link between atom names and atom types?
That is listed in the .rtp:
; name type charge cgnr
CG opls_235 0.500 3
The thing I wanna do is to figure out the bond parameters(b0,bk), and so
the angle, dihedral parameters in oplsaa FF.
Is it possible to give me some examples, such as the bond between CG and
OG1 in [ASN] in ffoplsaa.rtp?
The easiest thing I can think of to do is use the -pp flag with grompp, and look
at the processed topology, which will explicitly print the parameters.
Otherwise, you have to interpret atom types from the .atp and apply them to
generic atom types in ffoplsaabon.itp (which can take quite a bit of time!), so
let grompp do the work for you, and use that as a reference.
-Justin
thanks
Qiang
Justin A. Lemkul wrote:
friendli wrote:
Dear all,
To understand the exact parameters used in oplsaa force field, I read
the ffoplsaa*.*** files.
But I can not find all the corresponding atom types in the
ffoplsaa.rtp and ffoplsaabon.itp files.
for example, in rtp file, there is a bond between atom type CG and
OG1. But in *bon.itp, there is no such atom types CG or OG1 in the
[bondtypes]. where is the bond constants etc kept? and how Gromacs
find them?
CG and OG1 are atom names, not atom types. The force field can
determine bonds based on atom types. As long as they are recognized
atom types and parameters for such a bond are present, there will be
no problem.
-Justin
Can anybody give a hint for this?
thanks in advance
Qiang
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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