[gmx-users] Adding residue to .rtp file
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
Justin A. Lemkul, Ph.D.
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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