[gmx-users] question about topologies

Justin Lemkul jalemkul at vt.edu
Tue Oct 21 18:45:08 CEST 2014

Most of your questions are basic (bio)chemistry; I would suggest consulting some 
textbook material before diving into simulations, which add another layer of 

On 10/21/14 12:30 PM, Marcello Cammarata wrote:
> Hi,
> i am studied the capter 5 about topology, and o did not understand some aspect:
> 1-in the a.tp file, what does means the number after the simbol?

Atomic mass.

> 0   15.999 (C==0)
> OM  15.99  (CO)
> C   12.01  (C=0, C-N)
> 2- witch differences are between O and C?

O is oxygen, C is carbon.  Note these are the letter O, not the number zero. 
Different atom types are used depending on the chemical nature of the functional 
group.  For instance, O is used for carbonyl and amide groups.  OM is for 
carboxylic acids (deprotonated).

> 3- The file with the virtual sites what estention need to have?


> 4- in the manual is presented a case of a rtp file of [GLY] according with the
> structure that is C2H5NO2
>    so questions are:
>    a) there is a -C in the last row. Is this C part of the molecule?

The minus prefix indicates the previous residue, i.e. the peptide bond in the 

>    b) Why the group CH2 is called CA?

"Alpha carbon" is standard biochemical nomenclature, then positions are named 
with Greek letters down the chain - beta (CB), gamma (CG), etc.

>    c) What differences are between C and O, if both are C=0?

I don't understand this question, aside from the fact that C and O are different 
atoms.  They form a double bond (hence C=O) in several functional groups.



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


More information about the gromacs.org_gmx-users mailing list