Feature/imc #31

anaome · 2015-12-03T09:21:57Z

Hi Adrien,

Would you still be interested in considering the different changes and additions I made to implement the IMC FF into Ptools?
I would be very glad if you could guide me into what remains to be done to get the IMC FF working. So far, the reduction procedure is working and I get imcforcefield.h/.cpp to compile.

I am far from being good at programming and I am new to GitHub so please be indulgent ;-)

Best regards

Aymeric

chain I from 1CGI PDB file. Hydrogens added with gromacs pdb2gmx (amber99). ../PyAttract/reduce.py --ff imc ligandH.pdb > ligandH.red

chain E from 1CGI PDB file (with hydrogens). ../PyAttract/reduce.py --ff imc receptorH.pdb > receptorH.red

imc FF parameters

copy/paste of scorpionforcefield.pyx with Scorpion->Imc

copy/paste of scorpion_lbfgs.pyx with Scorpion->Imc

include imc files

the IMC FF is defined up to a cut-off distance of 15 Angström.

minimizer for IMC (ImcLbfgs just a copy of Lbfgs)

maigainin peptide one of dimer

magainin peptide two of dimer

anaome added 30 commits December 2, 2015 23:46

Update reduce.py

0a57d30

Create reduce_imc.py

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Create at2cg_imc.dat

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Update attract.py

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Update attractrigidbody.h

bb98154

Create imcforcefield.cpp

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Create imcforcefield.h

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Update setup.py

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Create ligandH.pdb

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chain I from 1CGI PDB file. Hydrogens added with gromacs pdb2gmx (amber99). ../PyAttract/reduce.py --ff imc ligandH.pdb > ligandH.red

Create receptorH.pdb

386fe53

chain E from 1CGI PDB file (with hydrogens). ../PyAttract/reduce.py --ff imc receptorH.pdb > receptorH.red

Create imc.par

c5535f3

imc FF parameters

Create imcforcefield.pyx

1d012b2

copy/paste of scorpionforcefield.pyx with Scorpion->Imc

Create imc_lbfgs.pyx

ea4fa9b

copy/paste of scorpion_lbfgs.pyx with Scorpion->Imc

Update _ptools.pyx

5013cd0

include imc files

Update imcforcefield.cpp

e25cfbd

Delete imcforcefield.cpp

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Create imcforcefield.cpp

1e41574

Update imcforcefield.cpp

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Update imcforcefield.cpp

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Update at2cg_imc.dat

f0f8e3c

Update at2cg_imc.dat

43e5dca

Update at2cg_imc.dat

6d569e0

Update at2cg_imc.dat

410f391

Update imcforcefield.cpp

940aae9

Update attract.py

ebb96db

the IMC FF is defined up to a cut-off distance of 15 Angström.

Update attract.py

154def5

minimizer for IMC (ImcLbfgs just a copy of Lbfgs)

Update imc.par

193ce90

Delete imcforcefield.cpp

4d141d3

Create imcforcefield.cpp

517faaa

Create mag1.red

e9d8952

maigainin peptide one of dimer

anaome added 2 commits December 17, 2015 12:33

Create mag2.red

15e9e93

magainin peptide two of dimer

Create attract.inp

e98dddb

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Feature/imc #31

Feature/imc #31

anaome commented Dec 3, 2015

Feature/imc #31

Are you sure you want to change the base?

Feature/imc #31

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anaome commented Dec 3, 2015