[gmx-users] Adding residue to .rtp file

Justin Lemkul jalemkul at vt.edu
Tue Oct 30 02:13:48 CET 2018

On 10/24/18 2:46 PM, Raji wrote:
> Thank you for your reply. I have few more questions
> 1. Yes, command pdb2gmx continued and generated the topology. The warning
> is about 74 atoms which are from the new added rtp entry. I just want to
> understand more about the warning. I dont find any related information?

Low or zero experimental occupancies indicate potentially problematic 
coordinates. If you're simply modeling in coordinates, the warning is 

> 2. What is the significance of the atom types in the rtp file?
> for example
> CTL3 - carbon of methyl group

This is from the lipid force field.

> CG331 - Aliphatic C for methyl group

This is a CGenFF type (any type with "G" as the second character is from 

> What is the difference between them and How to choose the right one for
> carbon in alkyl chain?

An alkyl chain on an amino acid should use CT1, CT2, CT3 (see existing 
amino acids).



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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


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