Dear gromacs users I have prepared a complex system consists of a protein and carbohydrate in lipid membrane using the KALP-membrane tutorial. After concatenating the three coordinate files, I visualized using VMD, but around 18 lipid atoms and more than 25 water molecules are joined with my protein residues as well as carbohydrate.
I proceed to energy minimization and it stops after reaching a step at ~500, showing high energy on one atom. My question is how to rectify this. I visualized using VMD and manually delete fused lipid and water molecule, but it creates large volume in membrane. I could not move forcefully because it disturb the conformation. Is any other way to correct it before proceeding to next phase. Thanks in advance, -Shine -- ---------------------------------------------------------------------- Shine Devaraj Assistant Professor Department of Biotechnology & Bioinformatics Dr. D Y Patil University, Navi Mumbai Associate Staff University of Central Lencashire, Preston, UK E:Mail: shinedev...@dypatil.edu,shin...@rediffmail.com Contact: (0)9320368486 Off: 022-39286142 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
