[gmx-users] Topology regarding

Justin Lemkul jalemkul at vt.edu
Fri May 10 18:23:07 CEST 2019

On 5/10/19 11:22 AM, RAHUL SURESH wrote:
> Hi gromacs users.
> To simulate a non-protein, (definitely not a small molecule), a molecule
> with 200 atoms, composing of C, N and H only, any suggestions to start with
> the groundwork?
> Precisely, if I am starting with updating the ff, ie to update the rtp
> entry for the molecule in atomtypes.rtp, is it compulsory to name the
> repeating atoms with different names?

Yes. If you tell pdb2gmx to bond "C" to "H" and you have a dozen "C" and 
two dozen "H," how will the program know which ones to connect?

> Can i name all the carbon to be C and Nitrogen to be N and Hydrogen to be H?


> Should I also update bonded and nonbonded files and hdb files?

If you introduce new parameters, you need to add them to the relevant 
files. If you need pdb2gmx to build your H atoms for you, you need to 
write an .hdb entry.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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