Dear Daniel
Many thanks for your help. It works now!
Best regards,
Maryam
From: Daniel Roe <daniel.r.roe.gmail.com>
To: Maryam Hamzehee <maryam_h_7860.yahoo.com>
Sent: Sunday, 29 January 2012 10:02 PM
Subject: Re: [AMBER] problem with SASA calculation
Hi,
The issue here is that when you perform this strip:
1: [strip !(:57-72)]
The atoms are renumbered, so that the first atom of old residue 57 is
now new atom 1 of new residue 1. However, since everything that
remains is what you want to calculate the surface area for you should
just be able to specify surf with no mask and the calculation will be
fine, e.g.:
trajin prod1.mdcrd 1 1 1
strip :WAT,:Na+,:Cl-,:ZNA
strip !(:57-72)
surf L out sasa.dat
Let me know if that works for you. Good luck!
-Dan
On Sun, Jan 29, 2012 at 8:31 AM, Maryam Hamzehee
<maryam_h_7860.yahoo.com> wrote:
> 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
>
>
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Mon Jan 30 2012 - 03:30:02 PST
