Dear users, I am new to GROMACS and i have just been practising with several tutorials. I am trying to do a molecular dynamics simulation of cysteine proteases an example falcipain-2 (PDBID=2OUL) and got several issues to pose 1) looking at the structure it has water molecules - do i get rid of the water molecules before starting the whole process 2) when i generate the topology file, i get several .itp files corresponding to each chain. Which one do i use for subsequent steps? 3) How do i handle the presence of disulphide bonds and salt bridges in my MD simulation process? 4) i will be glad if anyone grants me a tutorial which can help me in this.
Thank you. -- *MUSYOKA THOMMAS MUTEMI** B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science (Nagasaki University)* *PhD Student-Bioinformatics (Rhodes University) *Skype ID- MUSYOKA THOMMAS MUTEMI Alternative email - thom...@sia.co.ke * "Do all the good you can, By all the means you can, In all the ways you can, In all the places you can, At all the times you can, To all the people you can, As long as ever you can." - John Wesley. * -- 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
