Dear All
Many thanks for your replies and useful recommendation, I forgot to say in my previous email that my system has zinc (i.e. ZNA in prmtop); I tried the suggestion proposed by Daniel, I used the following command:
/share/apps/amber11/exe/cpptraj dof1_na_solvated.prmtop cpptraj.in > cpptraj.log 2>&1
For my protein as receptor I used:
cpptraj.in :
trajin prod1.mdcrd 1 1 1
strip :WAT,:Na+,:Cl-,: ZNA
strip !(:1-56)
surf R :1-56 out sasa.dat
The result of SASA was written in sasa.dat file and it worked.
In the case of DNA as the ligand of system I did the same change as indicated above for my protein and also I stripped the zinc atom :
trajin prod1.mdcrd 1 1 1
strip :WAT,:Na+,:Cl-,: ZNA
strip !(:57-72)
surf L :57-72 out sasa.dat
It did not worked and gave the following error:
CPPTRAJ: Trajectory Analysis. V1.0.5
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from file cpptraj.in
[trajin prod1.mdcrd 1 1 1]
[strip :WAT,:Na+,:Cl-,:ZNA]
[strip !(:57-72)]
[surf L :57-72 out sasa.dat]
TRAJECTORIES:
[prod1.mdcrd] is an AMBER trajectory, Parm 0 (with box info) (reading 1 of 40)
Coordinate processing will occur on 1 frames.
PARAMETER FILES:
0: dof1_na_solvated.prmtop, 26334 atoms, 8394 res, box 1, 8325 mol, 8314 solven
t mol, 1 frames.
REFERENCE COORDS:
No reference coordinates.
No frames defined.
OUTPUT TRAJECTORIES:
No files.
ACTIONS: Initializing 3 actions:
0: [strip :WAT,:Na+,:Cl-,:ZNA]
STRIP: Stripping atoms in mask [:WAT,:Na+,:Cl-,:ZNA]
1: [strip !(:57-72)]
STRIP: Stripping atoms in mask [!(:57-72)]
2: [surf L :57-72 out sasa.dat]
SURF: Calculating surface area for atoms in mask [:57-72]
BEGIN TRAJECTORY PROCESSING:
----- [prod1.mdcrd] (1-1, 1) -----
.... Setting up 3 actions for dof1_na_solvated.prmtop ....
STRIP: Stripping 24950 atoms.
New parmtop contains 1384 atoms.
72 residues.
3 molecules.
0 solvent molcules.
STRIP: Stripping 877 atoms.
New parmtop contains 507 atoms.
16 residues.
2 molecules.
0 solvent molcules.
Error: Surf::setup: Mask contains 0 atoms.
WARNING: Setup failed for [surf L :57-72 out sasa.dat]: Skipping
...................................................
[||||||||||||||||||||||||||||||||||||||||||||||||||] Complete.
Read 1 frames and processed 1 frames.
OUTPUT:
DATASETS:
There is 1 data set: L
DATAFILE OUTPUT:
sasa.dat: L
Warning: DataFile sasa.dat: Set L contains no data - skipping.
Warning: DataFile sasa.dat has no sets containing data - skipping.
How can I fix this problem?
Cheers,
Maryam
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
To: Maryam Hamzehee <maryam_h_7860.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Saturday, 28 January 2012 6:59 PM
Subject: Re: [AMBER] problem with SASA calculation
Hi,
On Sat, Jan 28, 2012 at 4:21 AM, Maryam Hamzehee
<maryam_h_7860.yahoo.com> wrote:
> The interesting point is that :
> SASAR +
> SASAL = SASAC
>
> 3952.9418 + 2466.6582 = 6419.6000
> Why?
As stated in the AmberTools manual, the surface area calculated by
cpptraj 'surf' reflects the contribution of atoms in <mask> to the
overall surface area, not the surface area of <mask> as an isolated
system, therefore it
is expected that the areas of R and L should sum
up to C. You could get SASA of each region by stripping everything
else out prior:
trajin prod1.mdcrd 1 1 1
strip :WAT,:Na+,:Cl-
strip !(:1-56)
surf R :1-56 out sasa.dat
Perform a run like that for each region you want the SASA for. Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Sun Jan 29 2012 - 06:00:04 PST
