[gmx-users] fails to minimization of ADP-protein

[Justin Lemkul]

On 8/30/19 6:10 AM, fatemeh.haghighi at univ-fcomte.fr wrote:
> Hi everybody
>
> I am doing a simulation of several ligands with a protein. one of
> ligands is ADP.
> I have optimized all ligands with gaussian, B3LYP method. then I used
> them for docking. the topologies for MD are constructed by
> antechamber, GAFF, adding AM1bcc charges method.
> I use gromacs 5.1.2 and forcefields Amber99SBILDN for all simulation.
> for all ligands, the simualtions ran without any problems. but for
> ADP, in the minimization step I have got the errors. I have copeid the
> EM results below.
> in addition, when I removed the partial charges from topology, the MD
> simulation ran without problems.
> I have used the ESP charges from gaussian, but nothing has changed.
> I have the same problem with 2MeSADP also.
> do you have any idea about that error? and how to overcome?
> thank you
> Steepest Descents:
> Tolerance (Fmax) = 1.00000e+01
> Number of steps = 20000
> Step= 0, Dmax= 2.0e-02 nm, Epot= -1.67454e+06 Fmax= 1.38745e+06, atom= 256680
>
> Step= 802, Dmax= 1.1e-06 nm, Epot= -5.33704e+06 Fmax= 1.06783e+05, atom= 7493
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 10 (which may not be possible for your system). It
> stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
>
> Steepest Descents converged to machine precision in 803 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy = -5.3370395e+06
> Maximum force = 1.3454029e+04 on atom 7489
> Norm of force = 6.5798233e+01
>

Your maximum force is very large, which suggests either a bad contact or 
a poor topology. Investigate what's going on around atom 7489 to see if 
there is a clash or otherwise develop and validate a better ADP topology.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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