GROMACS计算MMPBSA
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 filesPath 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 Inputsolvation energy parameter file. User may give choice ofeither polar-solvation or non-polarsolvationparametersfor both type of calculation. -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. -decompor-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。
$ ./configure --prefix=/home/cpu1710/apbs-1.3
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking target system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for --enable-fast option... no
checking for --enable-python... no
checking for icc... no
checking for pgcc... no
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... none
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) none
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking for ifort... no
checking for pgf77... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... no
checking whether gfortran accepts -g... no
checking if Fortran 77 compiler accepts -nofor_main... yes
checking if Fortran 77 compilers requires -nofor_main... no
checking how f77 mangles function names… configure: error: failed to compile fortran test program
大神求解救，急死了都
van der Waal energy = -240.118 +/- 18.741 kJ/mol
Electrostattic energy = -3204.902 +/- 79.035 kJ/mol
Polar solvation energy = 1051.308 +/- 41.322 kJ/mol
SASA energy = -24.182 +/- 0.938 kJ/mol
Binding energy = -2417.894 +/- 58.186 kJ/mol
飞天哥能不能帮我看下我这个结果，算得还算正常吗 您好，实在是着急又找不到资料，所以跑来特地向您请教一个问题：我想做一个蛋白质-配体复合体的动力学模拟，用PBSA来计算受体和配体之间的作用力大小；现在蛋白质在远离活性位点的一个位置上缺失一小段肽链（主链，包括七个氨基酸残基）。请问是否可以直接做动力学模拟？如需补全肽链，是否有推荐的软件？
先谢谢您啊！ 好东东，收藏啦 非常有价值：）感谢飞天兄的 分享！ 谢飞天哥 有了这个东西我终于可以睡个好觉了，大飞天哥。。 飞天大神，膜拜下 膜拜~~~~！ 你好，按帖子里的方法安装了gromacs和apbs，在安装g_mmpbsa时提示错误configure: error: Could not find /usr/local/lib/libapbsmainroutines.a library file
，缺少了库文件，请问如何添加进去？ 请问APBS库文件libapbsmainroutines.a, libapbs.a, libapbsblas.a,libmaloc.a, libapbsgen.a 和 libz.a是编译后就有的吗？ 问下这个程序可以做类似amber里面的自由能分解吗