Thank you for your help. I want to calculate binging free energy of small molecules to protein termini.
Steven On Thu, Aug 25, 2011 at 4:22 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 26/08/2011 1:16 AM, Steven Neumann wrote: > > Dear Gromacs Users, > > I want to do some simulations of the protein (its N anc C terminals) which > crystal structure does not exist. > > > There will normally be reasons why the termini do not have a defined > structure - often that this are in fact disordered. That will make your life > doing simulations considerably more difficult, and not just in choosing a > starting structure. > > > I submitted the sequence to www.proteinmodelportal.org obtaining > different structures based on different proteins from Protein Data Bank. For > instance my N terminal has 180 aa. Obtained models covers %Seq id of 78% for > 36 residues, 68% for 36 different residues, 62% of 36 another residues and > many other models below 50%. The website provides you with the PDB files of > your query so sounds perfect as you do not have to mutate every residue one > by one. > The question is whether this is efficent and provide a good result to use > such protein in my simualtions? Is this app. too big? > > > Depends what simulations you plan - but very likely you will not be able to > study more than one or two candidate structures. > > > What are the other ways to overcome this problem (obtain structure of the > protein which crystal structure does not exist? > > > Protein structure prediction is a field all of its own for a reason. It's > hard. > > Mark > > -- > 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 >
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