[AMBER] secstruct issue in CPPTRAJ

From: SARAH JEANNE LEFAVE <s.lefave.utah.edu>
Date: Mon, 8 Apr 2019 20:22:18 +0000

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

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?

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Received on Mon Apr 08 2019 - 13:30:02 PDT
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