On Jan 28, 2012, at 4:21 AM, Maryam Hamzehee <maryam_h_7860.yahoo.com> wrote:
> Dear Amber
> list
> I am trying
> to calculate the interface area in the complex of ligand (DNA) – receptor. I searched
> in the amber archive list; I found that "cpptraj"can be used for
> calculating of solvent accessible surface area (SASA). I used it as follows:
>
> /share/apps/amber11/exe/cpptraj
> dof1_na_solvated.prmtop cpptraj.in > cpptraj.log 2>&1
>
> cpptraj.in :
> trajin prod1.mdcrd 1 1 1
> strip :WAT,:Na+,:Cl-
> surf R :1-56 out sasa.dat
> surf L :57-72 out sasa.dat
> surf C :1-72 out sasa.dat
>
>
> The content of sasa.dat file is:
> #Frame R L C
> 1 3952.9418 2466.6582 6419.6000
>
> The interesting point is that :
> SASAR +
> SASAL = SASAC
>
> 3952.9418 + 2466.6582 = 6419.6000
> Why?
Because this is not doing what you think it's doing. The input file you have used above calculates the surface area based on the lcpo approximation for the receptor in the presence of the ligand and the ligand in the presence of the receptor -- not of the free receptor and free ligand. Thus, the sum of the receptor and ligand has to be the value for the complex.
You need three steps here. Calculate the complex, then strip the ligand and calculate the SASA of the receptor, then run cpptraj again and strip the receptor and calculate the SASA of the ligand. This should give you what you're looking for.
>
> I also found
> that another way for the calculation of surface area is defined as:
>
> Esurf = surften * total surf
This is not the surface area. The surface area is loosely proportional to the non-polar solvation free energy, which is what esurf is. Surften is just the proportionality constant that relates surface area to non-polar solvation.
> I also have
> got the binding energy for the ligand-receptor complex using the MMPBSA/GBSA
> (python version), If I use Esurf from the FINAL_RESULTS_MMPBSA.dat file, I have
> to consider a value for surften, we did not apply a value for surften in the mmpbsa.in file, so we have to use the
> default value for surften. Interestingly, I found that there are two default
> values for that (0.005 and 0.0072), which one can be used for this purpose.
The default value for the GBSA is 0.0072 kcal/mol/A**2 whereas it is 0.00548 or something for PB. This was done to preserve default values found in PBSA and the older perl version of MMPBSA for GB.
> Apart from
> this if I use either of 0.0072 and 0.005
> as default values, the values obtained by this method are different from the
> cpptraj approach.
For the reason I pointed out above.
>
> Another
> point and question:
> I also found
> in amber archive that Sander can be used for the SASA calculation.
> I used the
> following command:
> $AMBERHOME/exe/sander
> -O -i sasa.in -p dof1_na_solvated.prmtop -c dof1_na_solvated.inpcrd -x
> prod1.mdcrd -o SASA.out
>
> sasa.in
> &cntrl
> imin = 5,
> restraintmask=':1-73'
> #mask =
> :1-73
> /
> &gb
> gbsa = 1,
> surften = 1
> /
You are using the MMPBSA.py input file for sander, which is not correct. You can let MMPBSA.py generate an input file for you (just use the -make-mdins flag to avoid doing the actual calculation) and use that sander input file. Make sure you put use_sander=1 in your MMPBSA input file to get a sander input file.
HTH,
Jason
--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Jan 28 2012 - 08:00:03 PST
