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?
I also found
that another way for the calculation of surface area is defined as:
Esurf = surften * total surf
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.
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.
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
/
The SASA.out
file:
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on
01/28/2012 at 04:30:46
[-O]verwriting output
File
Assignments:
| MDIN: sasa.in
| MDOUT:
SASA.out
|INPCRD:
dof1_na_solvated.inpcrd
| PARM: dof1_na_solvated.prmtop
|RESTRT:
restrt
| REFC: refc
| MDVEL:
mdvel
| MDEN: mden
| MDCRD:
prod1.mdcrd
|MDINFO:
mdinfo
| MTMD: mtmd
|INPDIP:
inpdip
|RSTDIP:
rstdip
|INPTRA:
inptraj
Here is the input file:
&cntrl
imin = 5,
restraintmask=':1-73'
#mask =
:1-73
/
&gb
gbsa = 1,
surften = 1
/
error in reading namelist cntrl
How I can
fix this problem?
I was wondering if you could kindly help me in this regard.
Best
regards,
Maryam
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Received on Sat Jan 28 2012 - 01:30:03 PST
