Binding Surface in Molecular Dynamics
SurfinMD computes the binding surface area between a pair of chains as indicated in a reference structures. In addition it decomposes the binding area by residue, allowing the user to dig deep into the interactions.
There is an extensive documentation produced by Doxygen. Download and have fun browsing it :)
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# Program: SurfinMD - version 1.06p4 - 14Oct2016 #
# Diego E.B. Gomes(1), Gabriel Limaverde SCS(2) #
# Alan Wilter SS (3), Pedro G. Pascutti(4) #
# 1) INMETRO - Brasil #
# 2) Fundacao Oswaldo Cruz - Brasil #
# 3) EMBL - EBI, Wellcome Trust Genome Campus #
# 4) Universidade Federal do Rio de Janeiro #
# mailto: dgomes@pq.cnpq.br #
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Usage:
surfinmd -r ref.pdb -i traj.pdb -dcd traj.dcd -o surf.dat -or rsurf.dat -csv rsurf.csv -p 1.4 -d 1.0 -a 6
Please review all usage options [defaul]
-h = Display this help
-r = Reference Structure [ref.pdb]
-i = Input file [traj.pdb]
-dcd = Input file [traj.dcd]
-o = Output surface [surf.dat]
-or = Output surface/residue [rsurf.dat]
-csv = Output ALL surf/res [rsurf.csv]
-p = probe radius [1.4]
-d = probe density [1.0 A^2]
-a = attention number [6]
-ext = (Rvdw + ext ) [n]
-scal = (Rvdw * scal) [n]
LMDM - SURFINMD - version 1.06 - Fri Nov 20 11:38:58 BRST 2015
Developed by:
!debg ; Diego Enry B. Gomes, ; dgomes@pq.cnpq.br
!awss ; Alan Wilter ;
!gabriel ; Gabriel Limaverde S. C. Sousa ;
!melomcr ; Marcelo C. R. Melo ;
!pegepa ; Pedro G. Pascutti ; pascutti@biof.ufrj.br
Laboratorio de Modelagem e Dinamica Molecular
Instituto de Biofísica Carlos Chagas Filho - UFRJ
# Install
1. Edit "complile.sh" to select your favorite, and available compiler (intel is the fastest):
"g77,gfortran,intel32,intel64,sun"
compiler=intel64
2. If necessary, change the compiler path and flags
3. Run the compilation script " ./compile".
II) Usage
1. You need a PDB file with TWO diffent chain identifiers: A for the receptor and B for the ligand.
2. Parameters are passed through the command line.
3. Type "surfinmd -h" for more information.
WARNING: You MUST have only two chains: A and B !!!
III) Test
cd test/
./please.test
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Compared to PISA on 1BVE.PDB (I think it gives you the average of all frames)
chain1 chain2 area/a^2
A B 1583.8
B DMP 354.7
A DMP 348.2
Sum of chain A and B chains with DMP = 702.9
SurfinMD results
gfortran | Runtime = 8.588537 seconds
model 1 total area 654.5414
model 2 total area 620.0327
model 3 total area 694.4353
model 4 total area 673.0942
model 5 total area 697.4927
model 6 total area 698.9967
model 7 total area 731.1608
model 8 total area 682.5359
model 9 total area 727.3707
model 10 total area 648.9081
model 11 total area 726.0377
model 12 total area 692.0990
model 13 total area 675.2982
model 14 total area 685.4004
model 15 total area 658.2787