poltype2

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I'm preparing the force field for a covalently modified serine residue using poltype2. My aim is to use parameters from amoeba18bio to describe the serine backbone to ensure compatability, and...

Blossomstripe

So I have prepared the forcefield for 1,1-dimethyl urea molecule using poltype2. But could not do the energy minimization of aqueous solution of 1,1-dimthyl urea properly. Here is the output...

heman3333

Hi, I am parametrizing a drug-like ligand with Poltype2 and it seems to take several days which exceeds the time limit on my cluster. I am wondering if there is...

Ericwang6

the parameter of the heme cofactor in Its ferrous and ferric Forms

2

Can poltype2 generate the parameter of the heme cofactor in Its ferrous and ferric Forms? As shown below(Fe3+ is six-coordinated, and binds to residue CYS）: 

Cynthia-0807

Installation

4

Hello! I read through the README_INSTALL.MD and don't feel like I learned anything about how to install poltype2 I already have Tinker 8.10.5, gaussian16 and gdma installed so I didn't...

zimb3l

Large molecule has final charge

2

Hey Brandon, I was running poltype for 90 atom molecule and the `esp` from Psi4 keep getting killed with the basis used in poltype, so need to use less memory...

BJWiley233

From Poltype2 documentation, it seems that it is capable of creating force field parameters to simulate neat liquid. If I understand it correctly, it is able to adjust charges and...

cdpoon

Hi! When torsion parameters are computed _ab initio_ in a fragment, poltype produces those kind plots reporting the energy scan in the torsion and the fit results: Actually a plot...

DanieleQubit

There is one torsion parameter that was added to tinker [here](https://github.com/TinkerTools/tinker/commit/5c37bcd20cae2d215e99c8b066658eabf4bce9a2#diff-efc5d62366693141f795c79f47c5535dab174acb157f47f9021d9f63ec45632e) that is missing from poltypes2's [amoebabio18.prm](https://github.com/TinkerTools/poltype2/blob/master/ParameterFiles/amoebabio18.prm) for C-terminal threonines. There were actually 8 more updates as well since then...

BJWiley233

Just a heads up that the ```def FindDimensionsOfMoleculeTinker(poltype,structurefilepath):``` function in boxsetup.py necessarily fails to read the final.xyz generated by the ab initio fitting because of the 'xxx' title added by...

ghost