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Thanks Martin, In fact I used a decreased membrane surface tension during the simulation, as well as a decreased length membrane to mimick POPC and otherwise the same values for the remaining parameters: sigma_membrane -0.03 born_mode [1=exp 2=gauss] 2 sasa_mode [0,1=v(z) 2=gauss 3=exp] 3 v(z)_mode ...

During MC simulations, when using the option "v(z)_mode [1=linear 2=gauss 3=exp] 2 " I get the following message in the log.txt file: Info: negative born radius (too many terms in descreening sum - use cutoff) t = 0 rbinvf = -0.00251 (ATOM: 790 HA 90 VAL) and the calculated Born radius for...

I use the following formulae to go from the V1-V3 (used in Hippo) to U1-U6 (used in GROMACS) with CA-CA-OH-HH as example: ------------------------------------------------------------ In Hippo: V1 V2 V3 For CA-CA-OH-HH : 0 1.682 0 In GROMACS U1 U2 U3 U4 U5 U6 For CA-CA-OH-HH : 7.037 0 -7.037 0 0 0 In...

I am using GBIM with some explicit solvent molecules included into the active site. Is it possible to apply some positional constraints on these water molecules to prevent them to go away from the active site? I have not seen so far any way to add constraints within Hippo.

I tried to include the water molecules (TIP3P) inside the active site of a target protein, but when running an MC simulation it crashed (segmentation fault). In fact all the parameters for OW-HW and HW-OW-HW were set to 0 in the file oplsaa_forcefield.dat. After correcting them I still got the same ...

Regarding DIHEDRALS/IMPROPER DIHEDRALS. I am not sure how improper are taken into account by Hippo. Is there an easy way to go from the harmonic formulae K(theta-theta0)**2 to the V1-V3 coefficients?

When performing some MC simulations, I added my own ligands. For one of them I had missing parameters (new atom types) and I had therefore to add them in the oplsaa_forcefield.dat file. When looking at the 'DIHEDRALTYPES:' section, it is written 'Type V1 V2 V3 V4', but in fact it seems that the para...

OpenMP numthreads: While performing a MC simulation I tried to change the number of threads used, but the speed was never affected [using 0,1,4 or 8]. In fact it seems that Hippo uses the maximum number of threads available on one node regardless the value of 'OpenMP numthreads'. Also, when I teste...