Re: [AMBER] atom type of Sulphur in CYS/CYM (MCPB)

From: Ben Roberts <>
Date: Mon, 26 Mar 2012 07:02:04 +1300

To expand on Tong Zhu's remarks:

Executive summary: You should be OK, provided you don't need non-standard parameters between the SH and the rest of the cysteine residue.

Now, the lengthy explanation:

First, if you're in any doubt as to whether the "default" atom types are OK, you can create a "copy" of CYM, give it a new name, and change the atom types in the new residue type you've just created.

Second, the fact that the types overlap matters a lot less than you might think. Amber doesn't connect the partial charge to the atom type at all. And this is necessary, because the partial charge is much more likely to significantly change based on relatively small differences in chemical environment than the bonding parameters are. The atom type is really used to determine everything but the charge, viz., bond length and stiffness, angle size and stiffness, torsional parameters, and Lennard-Jones parameters.

So, does the fact that the atom type is SH instead of a "unique" atom type matter for these other parameter types? Well, except for the van der Waals parameters, not really. Because bonds are categorised by pairs of atom types, angles by threes, and proper dihedrals by at least two (in which case two wild cards are used) and possibly as many as four. So, for instance, by adding a new parameter for the SH-M bond, you won't override any existing parameters involving SH (well, unless your force field already contains such a bond type).

Hope that helps,

On 23/03/2012, at 10:12 PM, Tong Zhu wrote:

> Sorry for my poor english, but i think the most difference between CYM
> and CYS is that there is no H atom bond to S atom, so if you choice CYM
> as the residue name, the parameters of the CYM will be used by TLEAP(or
> XLEAP). And MCPB will assign new charge and force field parameters for
> the Metal binding group.
> On 03/23/2012 02:39 PM, ashwini gupta wrote:
>> Dear AmberUsers,
>> I am trying to generate metal site parameters. I have a cysteine in the
>> metal site and the sulphur of cysteine coordinates with the metal ion. As,
>> a result I have to rename CYS to CYM, since it interacts with a metal.
>> However when i see the atom type of Sulphur for both CYS and CYM in the
>> amino94.xml file they are the same, SH but their atm charge values are
>> different. Is this a bug. How can MCPB differentiate between two atom types
>> with the same name????
>> for CYM
>> <atom atmCharge="-0.736" bond12="5" bond13="3" bond14="1" bondAngle="116.0"
>> bondLength="1.81" bondTorsion="180.0" chain="E" identity=" SG " index="8"
>> type="SH" />
>> for CYS
>> <atom atmCharge="-0.3119" bond12="5" bond13="3" bond14="1"
>> bondAngle="116.0" bondLength="1.81" bondTorsion="180.0" chain="S"
>> identity=" SG " index="8" type="SH" />
>> Regards
>> Ashwini
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Received on Sun Mar 25 2012 - 11:30:03 PDT
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