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

From: ashwini gupta <>
Date: Mon, 26 Mar 2012 10:03:53 +0530

Dear Ben & Tong,

Thanks for the reply. I do understand that the only difference between the
two atoms in CYS and CYM is with respect to charges. I actually need to
build a non-standard residue, mimicking CYM and assign the sulphur atom of
the new residues atom type, SH. Thus I was wondering, whether it picks up
the SH details of CYM or CYS.

I am facing another problem, again with charges on the carbon atom and i
guess this problem, could be because of the atom type SH having different

As already explained the metal centre contains a CYS residue which forms a
coordinate bond with the metal using the SG and O. Please find the mol file
of the metal centre attached (metal_centre.mol).

When I use CYM to define CYS, I get very weird values for the charges on
Carbon (CG and CB) for all residues. As an example,
for restraint = 2 , i get CG of MET = 3.25465 and CB for CYS = 1.10889
for restraint = 1 , i get CG of MET = 3.04881,and CB for CYS = 1.92083
for restraint = 0, i get CG of MET = 2.96875,and CB for CYS = 2.08634

I am also attaching the three xml files generated using MCPB.

When i used CYX instead of CYM ( although i should not be using it since it
only defines cys with disulphide bridges), I get normal charge values, but
I end up with a system with some non-integral charge (~ -0.311). Although
the topology files are generated, i cannot even start any equilibration
simulation (after two rounds of minimization), as it gives the following
shake error

vlimit exceeded for step 49; vmax = 31.9392
vlimit exceeded for step 52; vmax = 112.2335

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 1 650 1279 1280

I guess this problem arises because the system is not completely

I have earlier performed one successful metal site parameterization ,
followed by simulation, so i dont think thr is a problem with the protocol
that i am using. I have a feeling that somehow the charge calculation are
creating this whole problem.


On Sun, Mar 25, 2012 at 11:32 PM, Ben Roberts <> wrote:

> 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,
> Ben
> 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
> >> _______________________________________________
> >> AMBER mailing list
> >>
> >>
> >
> >
> > _______________________________________________
> > AMBER mailing list
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> >
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Received on Sun Mar 25 2012 - 22:00:03 PDT
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