[gmx-users] on atomtypes
jalemkul at vt.edu
Thu May 12 17:20:24 CEST 2016
On 5/12/16 11:17 AM, Brett wrote:
> Dear All,
> Following is the part of the atomtypes.atp for gromos54a7:
> O 15.99940 ; carbonyl oxygen (C=O)
> OM 15.99940 ; carboxyl oxygen (CO-)
> OA 15.99940 ; hydroxyl, sugar or ester oxygen
> OE 15.99940 ; ether or ester oxygen
> OW 15.99940 ; water oxygen
> N 14.00670 ; peptide nitrogen (N or NH)
> NT 14.00670 ; terminal nitrogen (NH2)
> NL 14.00670 ; terminal nitrogen (NH3)
> NR 14.00670 ; aromatic nitrogen
> NZ 14.00670 ; Arg NH (NH2)
> NE 14.00670 ; Arg NE (NH)
> C 12.01100 ; bare carbon
> CH0 12.0110 ; bare sp3 carbon, 4 bound heavy atoms
> CH1 13.01900 ; aliphatic or sugar CH-group
> CH2 14.02700 ; aliphatic or sugar CH2-group
> CH3 15.03500 ; aliphatic CH3-group
> CH4 16.04300 ; methane
> CH2r 14.02700 ; CH2-group in a ring
> If I need to insert a new type list for example HS14 with weight 1.0080, should the word description of the atomtype (for example, "CH2-group in a ring" for "CH2r 14.02700") should be accurate or just a kind of reminder which the gromacas will not read?
It's a comment; it's not used for anything. Note that atomtypes.atp is only
read by pdb2gmx, so if this is related to your earlier post (and if it is, it's
better to continue a thread than to start a whole new topic) then you don't need
to be editing this file. You need to be adding parameters in ffnonbonded.itp or
the ligand's .itp file itself.
> In addition, the atomtypes.atp is a readonly file in /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/. WIll you please let me know how to save it after the HS14 atomtype was added?
Make a local copy of the directory, acquire admin privileges, or (most simply)
add missing parameters into the ligand's .itp file.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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