On Fri, May 17, 2013 at 10:21 PM, Shima Arasteh <shima_arasteh2...@yahoo.com > wrote:
> > Hi, > I am simulating a system composed if POPC , peptide, waters and ions. > I used the InflateGRO methodology to construct the system. > There are 2 phenylalanine residues in my peptide. Each phenyl has 2rings > connected from one side. I don't understand. Phenylalanine has a single aromatic ring. > After inflategro one of the phenyl rings is normal, but the other is not > because What I see them in vmd, there are 2rings remain close to eachother > but the expected bonds between them are not visible. > Two phenylalanine residues are not expected to bond. > The top file shows the correct bonds and angles and ... . > I ran EM, NVT, NPT, and thought this problem would be solved but it is > still as well as before. > The EM was also ok and did not show high enegy or crash. > Does this problem relate to the vmd and its algorithms? Or there is a > problem with my system. > How would the rings look usual? How could I solve it? > Your description of your expectations of phenylalanine do not seem to make sense. :-) 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
