Re: [modeller_usage] Including a Thioester linkage
To: Modeller Caretaker <>,
Subject: Re: [modeller_usage] Including a Thioester linkage
From: João Rodrigues <>
Date: Thu, 5 Nov 2009 12:41:38 -0800
Ok, I got it. I'm checking the pages and I think I'm gonna make it. Kind of helps to have the hopes high :)
Another question though, maybe this is a bit out of the scope of MODELLER but:
PRES DISU -0.36 ! Patch for disulfides. Patch must be 1-CYS and 2-CYS.
ATOM 1:CB CT2 -0.10 ! ATOM 1:SG SM -0.08 ! 2:SG--2:CB-- ATOM 2:SG SM -0.08 ! / ATOM 2:CB CT2 -0.10 ! -1:CB--1:SG
So, I get the syntax but I fail to understand one thing. Is that number -0.36 the overall charge of the residue or something? Because in the CHARMM Struct.doc file it says:
[ATOM <I><atomname> <parameter type> <charge> ]
But it doesn't mention anything next to the PRES line. Is this a MODELLER specific thing? What happens if I leave it blank? Is there a way to generate this automatically? Or are these set values written down somewhere?
Sorry for all the questions, but I'm trying to figure out how this works and not just copy paste things..