Hi,
Can you send me off-list the gnuplot file in question? Thanks.
-Dan
On Mon, Apr 8, 2019 at 4:22 PM SARAH JEANNE LEFAVE <s.lefave.utah.edu> wrote:
>
> Hi all,
>
> I am working on a secondary structure analysis on a relatively small protein. I am using the following input with CPPTRAJ V.18.01 (have also tried with 16),
>
> parm ../prmtop.3phy_trans.parm7
> trajin ../3phy_trans_dry_auto.nc
> secstruct :1-10 out 3phy_trans_1-10_dssp.gnu
> secstruct :11-20 out 3phy_trans_11-20_dssp.gnu
> secstruct :21-30 out 3phy_trans_21-30_dssp.gnu
> secstruct :31-40 out 3phy_trans_31-40_dssp.gnu
> secstruct :41-50 out 3phy_trans_41-50_dssp.gnu
> secstruct :51-60 out 3phy_trans_51-60_dssp.gnu
> secstruct :61-70 out 3phy_trans_61-70_dssp.gnu
> secstruct :71-80 out 3phy_trans_71-80_dssp.gnu
> secstruct :81-90 out 3phy_trans_81-90_dssp.gnu
> secstruct :91-100 out 3phy_trans_91-100_dssp.gnu
> secstruct :101-110 out 3phy_trans_101-110_dssp.gnu
> secstruct :111-125 out 3phy_trans_111-125_dssp.gnu
> run
> quit
>
> When I open the files with gnu plot, i get the following error
>
> set cbtics 0.000 7.000 1.0
> "3phy_trans_101-110_dssp.gnu", line 5: increment must be positive
>
> I have modified that line in the file to be '1.000 7.000 1.0’ and can visualize the plot but have an unusually large number of residues that are categorized as “none”. This is inconsistent with what vmd categorizes the residues as where most of the “none” residues are shown at beta sheets. I know that secstruct uses the DSSP algorithm whereas VMD uses STRIDE that includes a dihedral parameter.
> Is it possible that the issue with format could cause the incorrect assignment of label to reside?
>
> Thanks,
> Sarah
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Received on Wed Apr 10 2019 - 11:30:05 PDT
