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本帖最后由 eming 于 2015-1-12 17:55 编辑
AMBER有一套可以计算MMPBSA的程序，像NAMD或者GROMACS也有一帮人喜欢给写个类似的程序，譬如PBSA的计算采用APBS，原理是行的通的，于是NAMD下就有iAPBS的程序（http://mccammon.ucsd.edu/iapbs/），GROMACS下也有，
参见及下载g_mmpbsa
http://rashmikumari.github.io/g_mmpbsa/
程序安装：
1，需要的文件
1. GROMACS 4.5.x
Required Libraries : libgmx.a, libgmxana.a 和 libmd.a
2. APBS 1.2.x or 1.3.x
Required Libraries : libapbsmainroutines.a, libapbs.a, libapbsblas.a, libmaloc.a, libapbsgen.a 和 libz.a
这个在Gromacs和APBS编译之后是有的。APBS里能用OpenMP进行并行计算，通过环境变量控制使用的核/处理器数目，
export OMP_NUM_THREADS=X
Installation1.
Configure to installTo get detailed options ./configure --help Defining Path to GROMACS and APBS headers and libraries files Path to GROMACS include directory --with-gmx-include=/opt/gromacs-4.5.5/include Path to GROMACS Libraries files --with-gmx-lib=/opt/gromacs-4.5.5/lib Path to APBS Libraries files --with-apbs-lib=/usr/local/lib Path to APBS source directory --with-apbs=/opt/apbs-1.3-source Use above options/path to configure ./configure --with-gmx-include=/opt/gromacs-4.5.5/include --with-gmx-lib=/opt/gromacs-4.5.5/lib --with-apbs-lib=/usr/local/lib --with-apbs=/opt/apbs-1.3-source
2. make
make
3. Install
make install
详细用法请参见
http://rashmikumari.github.io/g_mmpbsa/Usage.html#g_mmpbsa
除了自己编译以外，官方网站现在已经提供已经编译好的执行文件，需要的话可以直接下载http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html
g_mmpbsag_mmpbsa calculates binding energy of biomolecular associations likeprotein-protein, protein-ligand protein-DNA etc using MM-PBSA. Itgives the different component of energy term in separate file so thatuser will have choice to have either MM, PB and SA energy values orall energies according to their objective. The tool also givesresidue wise contribution to total binding energy which will provideinformation about important contributing residues to the molecularassociation.
Onlymolecular mechanics (vdw and electrostatic) vacuum energy with energydecomposition g_mmpbsa -f traj.xtc -s topol.tpr -n index.ndx -mme -mm energy_MM.xvg -decomp -mmcon contrib_MM.dat Onlypolar solvation energy with energy decomposition g_mmpbsa -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -decomp -pol polar.xvg -pcon contrib_pol.dat Anexample mmpbsa.mdp isprovided in g_mmpbsa/test/polar_orig. Onlynon-polar solvation energy with energy decomposition g_mmpbsa -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -decomp -apol apolar.xvg -apcon contrib_apol.dat
An example mmpbsa.mdp for SASA model is provided in g_mmpbsa/test/sasa_orig. An example mmpbsa.mdp for SAV model is provided in g_mmpbsa/test/sav_orig. An example mmpbsa.mdp for WCA model is provided in g_mmpbsa/test/wca_orig.
Allenergetic term with energy decomposition g_mmpbsa -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -pbsa \ -mm energy_MM.xvg -pol polar.xvg -apol apolar.xvg -decomp \ -mmcon contrib_MM.dat -pcon contrib_pol.dat -apcon contrib_apol.dat Pleasekeep an eye on RAM usage because combined Molecular-Mechanics andPolar-Solvation energy calculation needs lots of memory.
FileOptions
-s topol.tpr Inputtpr/tpx file of molecule.
-f traj.xtc Inputtrajectory xtc/trr format file. WARNING:trajectory should be PBC corrected and molecule should not be PBCbroken. To make molecule whole in trajectory, please follow theselinks: PBC and trjconv.
-n index.ndx Inputatomic index file. User will get choice to select atomic groups.
-i grompp.mdp
-mm energy_MM.xvg vander Waal and electrostatic energy of the selected atom group/s. Ifthe index selected is for one group then the file will have vacuum MMenergy value for that group only. On the other side if two group isselected, then file will have vacuum MM energy values for bothselected group and for their complexes.
-pol polar.xvg Polarsolvation energy of the selected atoms group/s. If the index selectedis for one group then the file will have polar energy value for thatgroup only. On the other side if two group is selected, then filewill have polar energy values for both selected group and for theircomplexes.
-apol apolar.xvg Non-polarsolvation energy of the selected atoms group/s. If the index selectedis for one group then the file will have non-polar energy value forthat group only. On the other side if two group is selected fromindex file then file will have non-polar energy values for bothselected group and for their complexes.
-mmcon contrib_MM.dat VacuumMM van der Waals and electrostatic energy contribution per residueper frame/snaspshot.
-pcon contrib_pol.dat Polarsolvation energy contribution per residue frame wise.
-apcon contrib_apol.dat Non-polarsolvation energy contribution per residue frame wise.
Otheroptions -diff or -nodiff Default:yes Ifthis option is "yes", selection of two atom groups will beprompted. For example, atom group A and B is selected by user. Then,third combined AB group will be automatically generated. Further, allenergy calculation will be performed on these three atom groups A, Band AB. If it is switched to "no" by -nodiff,selection of only one atom group will be prompted and all energycalculation will be performed on selected atom group.
-mme or -nomme Default:yes Ifthis option is "yes", van der Waals and electrostaticenergy of the selected group/s will be calculated. This option can bechanged to "no" by -nomme toprevent this energy calculation.
-pdie 1 Valueof solute dielectric constant in the vacuum electrostaticcalculation. It should be similar to that of the polar-solvationenergy calculation.
-pbsa or -nopbsa Default:no :If this option is changed to "yes" by -pbsa,solvation energy will be calculated and solvation energy parameterinput file -i isnecessary for this calculation.
-rad bondi Threekeywords are accepted bondi, mbondi and mbondi2 whichcorresponds to three type of radius discussed in manuscript.
-ndots 100 Numberof dots per sphere used in the calculation of solvent accessiblesurface area and volume. Higher will be the number, more will be theaccuracy. -decomp or -nodecomp Default:no If this option is changed to "yes" by -decomp,energetic contribution of each residue to total binding energy willbe calculated using energy decomposition scheme.
---------------------------编译过程-----------------------------
g_mmpbsa的下载：
http://rashmikumari.github.io/g_mmpbsa/
--------compiling-Gromacs-4.5.5--------
GROMACS需要生成静态库编译
tar zxvf gmx-4.5.5.tar.gz
cd gmx-4.5.5
mkdir build
cd build
cmake ../ -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=/opt/gmx-4.5.5
make install
-------compiling-APBS-1.3--------------
g_mmpbsa目前不支持APBS-1.4,所以请下载1.2或者1.3
tar zxvf apbs-1.3-source.tar.gz
cd apbs-1.3-source/
./configure --prefix=/opt/apbs-1.3
make
make install
-------compiling-g_mmpbsa--------------
同样下载压缩包，解压后编译
./configure --with-gmx-include=/opt/gromacs-4.5.5/include --with-gmx-lib=/opt/gromacs-4.5.5/lib --with-apbs-lib=/usr/local/lib --with-apbs=/home/user/Downloads/apbs-1.3-source --prefix=/opt/g_mmpbsa
make
make install
需要注意的是apbs的编译, 如果环境变量含有ifort,它会自动选择用intel的ifort来编译，这样g_mmpbsa也应当使用ifort来编译.或者强制apbs采用gfortran等来编译。
如此以来也可以将NAMD的轨迹转换为gromacs的轨迹来计算MMPBSA。
拓扑文件可以使用psf2top.py来执行;
轨迹文件可以用mdconvert或者wordom来转换
Amber的拓扑文件/结构文件可以用acpype来转换
-----------------
还是强调如果自己不想编译；直接从官网站下载预编译好的就可以了。
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