Protein structure distorted after energy minimization using GROMACS

I have generated one protein structure from phyre2 using intensive mode. I tried to energy minimize it using GROMACS but unfortunately the resulting structure is completely distorted. Is there any way I can fix this problem? I appreciate your help on this.

energy-minimization

• 3,591 views • link

updated 4.2 years ago by Ram

• written 11.4 years ago by BI

1 answer

The information you have provided is very insufficient for any one to answer this or fix this problem. Possibly this might be a consequence of high temperature. Do the energy minimization with low temperature than the initial, then compare the result.

• 1 views • link

written 11.4 years ago by venu

More posts like this

Energy minimization beginner
written 6.4 years ago by Jennifer.Mutisya •

Hello Everyone, I am a beginner in Energy Minimization using Gromacs, could someone help me on how to carry out energy minimization of a homology …
protein 3D model not showing all AA residues
written 6.5 years ago by cocchi.e89

Maybe is a silly question but I found no clear information about. I generated the 3D models of a COL4A5 protein with a missense mutation …
About Energy Minimization
written 6.5 years ago by mahafujulislamtonmoy •

Recently I model a mutant protein. Now I want to obtain energy minimization. For this perpose I try gromacs but I can not do it …
Outliers residues in Ramachandran plot of predicted protein
written 9.1 years ago by l.souza

Hello everybody, I predicted the tertiary structure of a protein with Swiss-Model and Phyre2. Then, I refined the structure using ModRefiner. When I got a …
Modelling of proteins
written 9.5 years ago by shilpa.janarthanan •

My objective is to model a protein for which the experimental structure is not known. I performed homology modeling using Modeller and performed Energy Minimisation …
In silico interstitial deletion mutations in proteins
written 10.7 years ago by BI

How can one perform interstitial deletion mutations in silico in proteins. I tried using pymol but problem there is whenever I am removing a stretch …
Problem with executing do_dssp in gromacs
written 11.5 years ago by BI

I am new to *gromacs* and using *gromacs* 4.6.5 and *dssp*-2.0.4. When I am running these commands: export DSSP=/usr/local/bin/dssp do_dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc -o …
ab initio modeling reliability and protein-protein docking
written 11.6 years ago by BI

Hi. I have modeled one protein composed of peptide stretches from different proteins. I have used ab initio modeling to generate my model using phyre2 …
Energy Minimization Result Problem
written 12.3 years ago by nehabharty123 •

Hello I am new user of gromacs. I modeled a structure of protein with the help of Homology modeling and after that I validate the …
Docking After Energy Minimization - Receptor File Too Large
written 13.6 years ago by srikrish.sree •

I created a single amino acid change in a protein and energy minimized in gromacs using CG algorithm. After converting the file from .gro to …