[gmx-users] Adding residue to .rtp file

[Justin Lemkul]

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 
irrelevant.

> 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 
CGenFF.

> 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

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

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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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