Re: [AMBER] MD with emap restraints, restraints have no effect

From: Will Gerrard <will.gerrard.kuano.ai>
Date: Mon, 5 Jul 2021 09:53:15 +0100

Hi, thanks for your reply,

Sorry for being vague, maybe what i meant was "has no visible effect on the
dynamics of the supposedly restrained atoms", in that they move around as
if they had no restraint. There is some output relating to EMAP in the
output file:
"
Rigid 1 has 17 constrained atoms with mask: !.H= & :356;
                                              Rigid-fitting is not
requested for the constrained atoms.
    The constraint map is fixed in space.
Rigid 2 has 6 constrained atoms with mask: !.H= & :364;
                                              Rigid-fitting is not
requested for the constrained atoms.
    The constraint map is fixed in space.
"

and then each energy step looks like this:
"NSTEP = 900 TIME(PS) = 20.900 TEMP(K) = 405.78 PRESS =
0.0
 Etot = 86970528.8826 EKtot = 42629.4621 EPtot =
 86927899.4206
 BOND = 1220.5163 ANGLE = 3215.9085 DIHED =
 4909.8586
 1-4 NB = 1371.4549 1-4 EEL = 11996.3753 VDWAALS =
20692.5377
 EELEC = -172547.8655 EHBOND = 0.0000 RESTRAINT =
 87057040.6349
 EAMBER (non-restraint) = -129141.2143
 EMAP = 87057040.6349
"
Where the RESTRAINT value scales with the value of fcons in the input file,

I have tried a simulation where the starting coordinates are very different
from the restraint coordinates (10+A away) and one where they are much
closer (5ish A away) with the same result. In a smaller test simulation i
ran without the full protein the restraints do seem to have an effect, i
can fix the atoms in place using the same coordinates in the restraint as
in the input structure, and when i put in different coordinates the SER
residue im trying to restrain appears to move to a different position and
then be held there, but it is not the position specified in the restraints.

Running the full simulation (with the protein) using the input coordinates
as the restraint coords does not have the same effect, the simulation still
appears to run as if there are no restraints (despite the output looking
similar to the above)

Hope this provides some more information, is there anything else i can
test/check ?

Thanks,

Will
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Received on Mon Jul 05 2021 - 02:00:02 PDT
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