Hi all,
I stumbled across a problem analysing the trajectory of a peptide
containing non-standard amino acids using the surf function in cpptraj.
The non-standard residue is the first in the sequence (R1).
These are the commands I used in cpptraj:
parm DIM_solv.parm7
trajin DIM_solv_prod.crd
surf R1 :1 out sasa1.dat
...
surf R10 :10 out sasa10.dat
run
The cpptraj output looks like this:
ACTION SETUP FOR PARM 'DIM_solv.parm7' (10 actions):
0: [surf R1 :1 out sasa1.dat]
LCPO surface area will be calculated for 14 atoms.
14 solute atoms.
Warning: Using carbon SA parms for unknown atom 175 type Cl-
Warning: Using carbon SA parms for unknown atom 350 type Cl-
Warning: Using carbon SA parms for unknown atom 352 type Cl-
Warning: Using carbon SA parms for unknown atom 353 type Cl-
...
For R2 to R10 I the files sasa*.dat look fine, I receive one value per
frame. However for sasa1.dat I get 10 values per frame:
#Frame R
1 177.0622 140.8356 164.5719 57.5352 163.3728
122.6951136.7847 169.207108.0297 148.5364
...
This is what desc R1 gives me in tleap:
RESIDUE name: PCA
RESIDUE sequence number: 1
RESIDUE PDB sequence number: 1
Type: undefined
Connection atoms:
Connect atom 1: A<C5 7>
Improper torsions:
Contents:
A<H6 15>
A<H5 14>
A<H4 13>
A<H3 12>
A<H2 11>
A<H1 10>
A<O2 8>
A<C5 7>
A<O1 6>
A<C4 5>
A<C3 4>
A<C2 3>
A<C1 2>
A<N1 1>
>
How can I get cpptraj to print the SASA for the entire residue? Is there
something wrong with the parameter file?
Thanks in advance for your help!
Best,
Andy
--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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Received on Mon Mar 27 2017 - 05:30:03 PDT
