Can you clarify what you mean by "NAMD with Amber"? Is this a NAMD error,
or when you use Amber for simulations?
I would also see if the problem occurs without the ligand; often errors can
be a sign of issues with user defined force field parameters.
On Mon, Jul 8, 2019, 1:25 PM Bowman, Jacob <bowman.1334.buckeyemail.osu.edu>
wrote:
> 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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>
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Received on Mon Jul 08 2019 - 11:00:02 PDT
