MUSYOKA THOMMAS mutemibiochemistry at gmail.com
Wed Aug 21 22:00:21 CEST 2013

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.

B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science
(Nagasaki University)*
*PhD Student-Bioinformatics (Rhodes University)
Alternative email - thommas at sia.co.ke

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