On 7/19/13 8:20 AM, afsaneh maleki wrote:
Dear gmx users
I scrap lines from some files in oplsaa.ff folder as the following
ffnonbonded file:
[ atomtypes ]
opls_157 CT 6 12.01100 0.145 A 3.50000e-01
2.76144e-01
atomtypes.atp file:
opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols
also, I looked at /gromacs /Documentation/file format/.n2t that written:
To translate atom names into atom types, the x2top program uses library
files called .n2t files as input. These files contain information about
atom types, charges, and connectivity to neighbors. The format of such a
file is exemplified by:
*C* opls_157 -0.18 12.011 4 H 0.108 H 0.108 H 0.108 C 0.150
The above line interprets an atom named C to be the carbon atom in CH3,
CH2, or alcohols (atom type opls_157).
My question is that carbon atomname with opls_157 atomtype is *C* or CT?
The type is opls_157 for the purposes of ffnonbonded.itp, which is translated to
the CT in ffbonded.itp.
In other word the first column in .n2t is atomneme (CT as mentioned in
ffnonbonded file ) or element name (C as mentioned in file format.n2t )?
In Gromacs nomenclature, atom names are whatever is read from the input
coordinate file (no differentiation between atom name and element name) and atom
types are force field-specific.
Also, are 6, 8 10 columns atomname or element name?
Both, given Gromacs' interpretation of atom names. g_x2top will look for
matches based on whatever element it finds, so in the case of column 6, any of
these will match: H, HA, H1, H2, etc.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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