It seems the LCPO method does not have the parameters for those atoms hence it assigns carbon SA parameters to compute the SASA.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Andreas Tosstorff [mailto:andreas.tosstorff.cup.uni-muenchen.de]
Sent: Monday, March 27, 2017 5:59 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] surf cpptraj non-standard residue
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 - 06:00:04 PDT
