gromacs tutorial for simulation
beta lactamases...the numbers OXA-23, OXA-143, KPC-2, IMP-1 what these numbers are denoting?.
06 July 2017 6,755 2 View
I want to do MD simulation for metallo enzyme as well as protein-ligand complex in GROMACS. But when i use the pdb structure with zn ions it showing error. Help me to sort out this problem. Which...
10 November 2016 4,488 4 View
suggest tools to repair missing residues in PDB coordinate file
05 June 2016 2,694 2 View
In grompp in ion.trp filr creation there occur error. Fatal Error, Too much Warning (1), use option -maxwarn. could anybody tell me how to use this option, if i use this option its asking for...
02 March 2015 9,217 3 View
gromacs forcefield error
02 March 2015 7,032 2 View
rectify my error Fatal error:Atom HB3 in residue SER 3 was not found in rtp entry SER with 8 atomswhile sorting atoms.
02 March 2015 1,600 10 View
sybyl x protein - ligand complex
02 March 2015 210 2 View
I'm referring to molecular docking sybyl version 2.0
09 October 2014 8,334 5 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
I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance
03 March 2021 3,568 1 View
Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...
02 March 2021 2,431 3 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
Actually, I am running cfd simulation for a heat exchanger which has two fluids one hot and other one is cold fluid. there is a solid domain between them, which I removed and instead I have used...
01 March 2021 9,537 2 View
I am working on roof joint and trying to simulate the behaviour in Abaqus. I am successful in running the model but the final graph does not follow the experimental curve in the negative direction...
01 March 2021 6,661 3 View
