[gmx-users] question about gmx do_dssp

[YanhuaOuyang]

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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