[gmx-users] question about gmx do_dssp

[Mark Abraham]

Hi,

I'd start by checking if that last residue is a normal one...

Mark

On Sat, Aug 5, 2017 at 2:02 PM YanhuaOuyang <15901283893 at 163.com> wrote:

>
>
> Dear Mark,
>
>    Thank you, I have figure out the problem, but to my surprise, the
> output xpm file lack the information of the last residue for the CHARMM27
> force file (charmm's trajectory is good), but not for other force field. I
> wonder whether the DSSP program in the gromacs ignore the last residue of
> structures generated by CHARMM27 force field.
>
> Best regards,
> Ouyang
>
>
>
>
>
>
>
>
> At 2017-08-04 22:32:25, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
> >Hi,
> >
> >Isn't that figure what is in the xpm file?
> >
> >Mark
> >
> >On Fri, Aug 4, 2017 at 4:20 PM YanhuaOuyang <15901283893 at 163.com> wrote:
> >
> >> Hi,
> >>    I have run a MD simulation and used gmx do_dssp to calculate the
> >> secondary structure content. The output files are md_dssp.xpm and
> >> scount.xvg. I want to know that each residue  belongs to what kind of
> >> secondary structure for each frame. But the scount.xvg output file only
> >> have the number of residues with each secondary structure and the total
> >> secondary structure count as a function of time. So,  can I get the
> >> information on "each residue belongs to which kind of secondary
> structure
> >> for each frame" to draw a figure of " amino acid vs secondary
> structure" ?
> >>
> >> Best regards,
> >> Ouyang
> >> --
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