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

[fatemeh.haghighi at univ-fcomte.fr]

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