Re: [AMBER] Residues Naming Advice

From: He, Amy via AMBER <amber.ambermd.org>
Date: Wed, 14 Feb 2024 04:06:43 +0000

Hi Kaleem,

Residue CYM has a total charge of -1, whereas CYX has a total charge of 0. Even though they appear to have the same number of atoms, CYX is meant to be a disulfide-bond forming residue not just being deprotonated.
If you’re unsure check out the definition in: $AMBERHOME/dat/leap/lib/amino19.lib

Hope this helps

Bests, 


--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: Kaleem Arshad via AMBER <amber.ambermd.org>
Date: Tuesday, February 13, 2024 at 10:51 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Residues Naming Advice
Hi, Respected AMBER users, hope you are doing well. I need advice about using name for cysteine residues. In manual, there is no mention of CYM for depronated cysteine residue, while in tutorial, it's written. If I use CYM as name for depronated cysteines as determined by H++ server, then in creation of prmtop and inpcrd files, leap shows correct charge as determined by H++ server, while if I change CYM to CYX to avoid leap hydrogenating them, then leap tells that there is unperturbed charge. In both cases I added  Na+ to neutralize it as protein has -6 charge on pH 7.4 determined by H++ server. Wanna ask should I use CYM or change it to CYX?
Please see leap files attached.
Thanking you in advance for your help.
Kaleem Arshad
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Received on Tue Feb 13 2024 - 20:30:02 PST
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