How can I rectify the following error in Gromacs?

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In beta-lactamases..ex: OXA-23, KPC-3 ..etc., the number after the enzyme indicates what?

beta lactamases...the numbers OXA-23, OXA-143, KPC-2, IMP-1 what these numbers are denoting?.

06 July 2017 6,755 2 View

How to run MD simulation for metallo enzymes having zn in GROMACS?

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

If a PDB coordinate file has missing residues. How can i repair the protein?

suggest tools to repair missing residues in PDB coordinate file

05 June 2016 2,694 2 View

In GROMACS when I give a PDB file its showing the error that HE1 atom not found in topology. How can I rectify it?

gromacs forcefield error

02 March 2015 7,032 2 View

Can anybody send gromacs tutorial for protein - ligand complex MD simulation in ubuntu?

gromacs tutorial for simulation

02 March 2015 3,737 0 View

How can I rectify the following GROMACS error? Fatal error: Atom HB3 in residue SER 3 was not found in rtp entry SER with 8 atoms while sorting atoms.

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

How can I get a protein-ligand complex from sybyl x 2.0 for MD run and how can we separate the ligand from the protein?

sybyl x protein - ligand complex

02 March 2015 210 2 View

Why are we adding hydrogen, removing side chains and removing ligand substructure in molecular docking?

I'm referring to molecular docking sybyl version 2.0

09 October 2014 8,334 5 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

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

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

How to analyze a particular region of my simulation box in GROMACS?

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

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

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Why are the velocities so high in my Boussinesq approximation Fluent simulation?

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

What is the characteristic length to determine the Reynolds number for the scattered turbulent fluid flow?

Dear all, I just saw this example in FB on the difference between laminar flow and turbulent flow. The flow from a pipe hits the sink and scattered. The flow from the pipe is characterized as...

02 March 2021 1,999 5 View

Justin Lemkul

grompp prints out notes and errors. Notes are informative. Errors indicate something badly wrong with the input. You shouldn't use -maxwarn to simply circumvent the problem, you should rectify the error, whatever it is.

Malathi Kullappan

Thank you sir, i will try to rectify my error.

Aditya Kumar Sarkar

HI,

What error you are actually getting?