Search found 38 matches
- Wed Nov 12, 2008 7:00 pm
- Forum: Force field parameters
- Topic: spermine?
- Replies: 2
- Views: 35835
Re: spermine?
Ciao Kaihsu, I've built is from opls-aa amine parameters, check out the updated forcefield and database files. I also attach the PDB it builds. Please check that it's correct, (i also added the di-methyl-amine and di-ethyl-amine, from which i built it). Have fun and let us know how you fare ;) Best ...
- Wed Oct 08, 2008 9:53 am
- Forum: Bugs
- Topic: Novice assistance
- Replies: 6
- Views: 39853
Re: Novice assistance
Did you just put the three lines you quote in your post as input? Hippo needs the whole hippo_input.txt file with all the commands at the exact row and column as in the original file. If you want to change an option simply replace the corresponding command/number with yours. If you omit lines or mov...
- Fri Aug 29, 2008 8:09 am
- Forum: Bugs
- Topic: Negative Born radii with v(z) = 2
- Replies: 3
- Views: 14035
Re: Negative Born radii with v(z) = 2
The transrot scan will take your protein structure and rotate and translate it through the membrane (zmin->zmax, adjust dz, dtheta and dphi). It will then print out the insertion surface. This will tell you if the native state of the protein sits stably in the membrane (indicated by TST atoms in the...
- Fri Aug 29, 2008 7:58 am
- Forum: Feature requests
- Topic: MD simulations
- Replies: 2
- Views: 13655
Re: MD simulations
You can run normal MD (mode = MD simulation), the generalized Born membrane will be available in MD mode soon - needs some minor debugging...
- Fri Aug 29, 2008 7:56 am
- Forum: Running simulations
- Topic: MC steps and MD simulation time
- Replies: 5
- Views: 15579
Re: MC steps and MD simulation time
We have never tested a system of this size, so it's difficult to answer.
For smaller systems (20-30 residues) we found that one MC scan (i.e. the number of MC moves required to move every residue once) equals to roughly one 2 fs MD time step.
For smaller systems (20-30 residues) we found that one MC scan (i.e. the number of MC moves required to move every residue once) equals to roughly one 2 fs MD time step.
- Wed Aug 13, 2008 10:23 am
- Forum: Bugs
- Topic: Negative Born radii with v(z) = 2
- Replies: 3
- Views: 14035
Re: Negative Born radii with v(z) = 2
- The exponential can be better at keeping helices stable, so it's fine to use it. A good combination is often to use a Gaussian for the Born and V(z) term and an exponential for the SASA term. The following works well for e.g. WALP: born_mode [1=exp 2=gauss] 2 sasa_mode [0,1=v(z) 2=gauss 3=exp] 3 v...
- Thu Aug 07, 2008 2:40 pm
- Forum: Bugs
- Topic: TIP3P molecules included inside a cavity
- Replies: 1
- Views: 11487
Re: TIP3P molecules included inside a cavity
TIP3P water is hard coded for efficiency. It is not currently implemented for use with GB/SA. Your residue based water molecules is a good work around.
- Thu Aug 07, 2008 2:37 pm
- Forum: Force field parameters
- Topic: Which dihedral parameters are needed in oplsaa_forcefield
- Replies: 1
- Views: 16211
Re: Which dihedral parameters are needed in oplsaa_forcefield
Hippo uses only V1, V2, V3 as in the 1996 OPLS-AA forcefield paper
You can convert parameters from gromacs to hippo units using the attached excel sheet.
You can convert parameters from gromacs to hippo units using the attached excel sheet.