Dear Amber users,
I’ve been performing QM/MM molecular dynamics of a protein and its ligand. Afterwards, I’ve run cluster analysis to identify representative structures and continue the calculations from one of these structures.
In order to do so, I’ve extracted the coordinates of the structure I’ve chosen using the following script in cpptraj:
#Load topology and trajectories
parm native2.parm
loadcrd nat2_md-qm.nc name nat2-0
loadcrd nat-ew2-0_mdqm.nc name nat2-0
loadcrd nat-ew2-0_mdqm1.nc name nat2-0
loadcrd nat-ew2-0_mdqm2.nc name nat2-0
loadcrd nat-ew2-0_mdqm3.nc name nat2-0
loadcrd nat-ew2-0_mdqm4.nc name nat2-0
loadcrd nat-ew2-0_mdqm5.nc name nat2-0
loadcrd nat-ew2-0_mdqm6.nc name nat2-0
loadcrd nat-ew2-0_mdqm7.nc name nat2-0
loadcrd nat-ew2-0_mdqm8.nc name nat2-0
loadcrd nat-ew2-0_mdqm9.nc name nat2-0
loadcrd nat-ew2-0_mdqm10.nc name nat2-0
loadcrd nat-ew2-0_mdqm11.nc name nat2-0
loadcrd nat-ew2-0_mdqm12.nc name nat2-0
loadcrd nat-ew2-0_mdqm13.nc name nat2-0
loadcrd nat-ew2-0_mdqm14.nc name nat2-0
loadcrd nat-ew2-0_mdqm15.nc name nat2-0
loadcrd nat-ew2-0_mdqm16.nc name nat2-0
loadcrd nat-ew2-0_mdqm17.nc name nat2-0
loadcrd nat-ew2-0_mdqm18.nc name nat2-0
loadcrd nat-ew2-0_mdqm19.nc name nat2-0
loadcrd nat-ew2-0_mdqm20.nc name nat2-0
crdout nat2-0 nat2-0_3089.rst restart crdframes 3089,3089
Now that I want to pursue the QM/MM MD adding new residues to the QM region using the restart coordinates obtained with cpptraj and the topology file I was using from the beginning of my calculation, I get the following error message:
ERROR: I could not find enough velocities in
nat2-0_3089.rst
I guess I’ve made a mistake somewhere (as I’ve never extract coordinates using cpptraj), please help me correct it to continue my simulation.
Thanks in advance,
Ruth
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Received on Tue Nov 22 2016 - 09:30:02 PST
