[gmx-users] visualizing the system

[Mark Abraham]

On Fri, May 17, 2013 at 10:21 PM, Shima Arasteh <shima_arasteh2001 at 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