I have a problem - I do not know how to create topology and .gro for nonane. pdb2gmx says that my residue name is not known, and it's right because of course it's not a residue. Anyone know a solution for that kind of problem?
Thanks, i think You solved my problem (or at least led me to further problems :) ). I'll look for .itp for decane which I saw and will modify it.
I wasn't thinkink about FF yet (it's educational purpose).
I'm working on ethanolamine hydration energy simulation and it's really hard to find experimental value. Has anybody ever seen/know it and can help me?
09 October 2013 6,156 3 View
I'm very new to CHARMM parameteris in GROMACS. While reading topology files I saw a "multiplicity" section that gives several different params for the same dihedral angle. I'd like to know what...
07 August 2013 5,039 1 View
With my friends, I am going to write a script for GROMACS to make running simulations automatic. It will take a pdb file as an input and ask some questions. Elese will be done automatically. I...
04 May 2013 1,811 16 View
http://pridb.gdcb.iastate.edu/RPISeq/
01 February 2013 8,079 0 View
How to calculate the RMSD values for a MD simulation using MOE?
07 August 2021 0 0 View
When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.
16 June 2021 0 0 View
Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...
03 March 2021 9,989 2 View
Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...
03 March 2021 5,978 5 View
Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...
02 March 2021 4,910 3 View
Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...
02 March 2021 4,569 4 View