[gmx-users] on atomtypes

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================