Dear All,
I am trying to reproduce the hydroxy apatite tutorial (
http://ambermd.org/tutorials/advanced/tutorial27/hap_water.htm).
I tried to run the simulation using the files in the tutorial (hap16_water.prmtop andhap16_water.inpcrd and the input files hap16_water_min1.in,hap16_water_min2.in,hap16_water_heat.in,and hap16_water_prod.in), but got an error message in the output of the minimisation:
| Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
peek_ewald_inpcrd: SHOULD NOT BE HERE
I understand from the list that this indicates some problem with the .inpcrd file. I was using the AMBER14 simulation engine with AmberTools16 with update 13.
Next I tried to build the to build a solvated HAP system as described in the tutorial. I executed thehap_tleap.in script using the hap16.pdb and hap.mol2 files dowloaded from the tutorial, but leap does not find the required force field files:
-I: Adding /home/kris/bin/amber16/dat/leap/prep to search path.
-I: Adding /home/kris/bin/amber16/dat/leap/lib to search path.
-I: Adding /home/kris/bin/amber16/dat/leap/parm to search path.
-I: Adding /home/kris/bin/amber16/dat/leap/cmd to search path.
-f: Source build_hap16.leap.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./build_hap16.leap
Could not open file leaprc.interface_v1_5: not found
----- Source: /home/kris/bin/amber16/dat/leap/cmd/leaprc.water.spce
----- Source of /home/kris/bin/amber16/dat/leap/cmd/leaprc.water.spce done
Loading library: /home/kris/bin/amber16/dat/leap/lib/atomic_ions.lib
Loading library: /home/kris/bin/amber16/dat/leap/lib/solvents.lib
Loading parameters: /home/kris/bin/amber16/dat/leap/parm/frcmod.spce
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for SPC/E water
Loading parameters: /home/kris/bin/amber16/dat/leap/parm/frcmod.ionsjc_spce
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and SPC/E water from Joung & Cheatham JPCB (2008)
Loading parameters: /home/kris/bin/amber16/dat/leap/parm/frcmod.ions234lm_126_spce
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for SPC/E water model (12-6 normal usage set)
Loading Mol2 file: ./hap.mol2
Reading MOLECULE named HAP
Loading PDB file: ./hap16.pdb
total atoms in file: 704
(using default radius 1.500000 for H2)
(using default radius 1.500000 for H1)
(using default radius 1.500000 for O26)
(using default radius 1.500000 for O25).....
Indeed, there is no leaprc file there in the corresponding location. I tried it with AmberTools15/AMBER 14 and also I compiled AmberTools17 without the AMBER 16, in both cases I got the same error.
I downloaded the INTERFACE force field v 1.5 from INTERFACE MD, but there are no AMBER ff files in there, only for GRAMCS or CVFF. Reading the tutorial I thought that the INTERFACE ff was implemeneted for use in AMBER. I would appreciate if anyone could clarify these issues for me.
Best wishes,Kris
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INTERFACE MD
The Heinz team develops all-atom force fields to simulate nanostructures of 1 to 100 nm size in high accuracy, i... | |
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Received on Thu Aug 10 2017 - 03:30:02 PDT
