Hello Amber Users,
I am currently using NAMD with Amber to run a simulation of a protein/ligand complex in an octahedral water box with TIP4Pew water model.
The initial structure comes from the end of a previous simulation that is provided by a tutorial for the program SEEKR. TLEAP is used with this file:
"source /path/.conda/envs/conda_seekr5/dat/leap/cmd/leaprc.protein.ff14SB
source /path/.conda/envs/conda_seekr5/dat/leap/cmd/leaprc.gaff
source /path/.conda/envs/conda_seekr5/dat/leap/cmd/leaprc.water.tip4pew
set default FlexibleWater on
set default PBRadii mbondi2
loadoff /path/SEEKR/Tutorial/Ca2.lib
loadoff /path/SEEKR/Tutorial/benzamidine.lib
loadamberparams /path/SEEKR/Tutorial/benzamidine.frcmod
WAT= T4E
HOH= T4E
loadAmberParams /path/.conda/envs/conda_seekr5/dat/leap/parm/frcmod.ionsjc_tip4pew
loadAmberParams /path/.conda/envs/conda_seekr5/dat/leap/parm/frcmod.tip4pew
holo = loadpdb /path/SEEKR/Tutorial/root_dir/anchor_2_2_site1_-1.1_19.6_18.3_0/md/holo_wet.pdb
bond holo.7.SG holo.137.SG
bond holo.25.SG holo.41.SG
bond holo.109.SG holo.210.SG
bond holo.116.SG holo.183.SG
bond holo.148.SG holo.162.SG
bond holo.173.SG holo.197.SG
charge holo
check holo
saveamberparm holo /path/SEEKR/Tutorial/root_dir/anchor_2_2_site1_-1.1_19.6_18.3_0/md/building/holo2.parm7 /path/SEEKR/Tutorial/root_dir/anchor_2_2_site1_-1.1_19.6_18.3_0/md/building/holo2.rst7
savepdb holo /path/holo_leap.pdb
quit
"
I get the note:
Note: 1-4: angle 23026 23027 duplicates bond ('triangular' bond) or angle ('square' bond)
For nearly all the water molecules.
Then I am able to run a minimization for the water molecules with the protein/ligand atoms fixed.
When I move on to a temperature equilibration stage, I run into the error:
Atoms moving too fast - and they are all exclusively the EPW atoms. I have run the minimization for longer and tried to reduce the temperature on the temperature equilibration to no avail. Is there any way to overcome this issue? I have tried this same scheme with the TIP3P model and it works just fine. I'm not sure where the error with the TIP4Pew is coming from.
Jacob Bowman
OSBP Graduate Student
Lindert Lab
Department of Chemistry and Biochemistry
2116 Newman Wolfrom
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Received on Mon Jul 08 2019 - 10:30:02 PDT
