⑴ 如何在ubuntu上安裝namd
是的，要先解壓。終端輸入：sudo tar -zxvf 壓縮文件名.tar.gz /tmp（假設想解壓到/tmp目錄），然後cd 解壓後的目錄名 進入解壓後的目錄，ls查看其中有沒有INSTALL文件，按照上面的說明安裝即可。一般步驟是：sudo ./configure、make、make install
⑵ centos 無法解析域名怎麼辦
應該是一個叫named的服務沒有開啟，可以使用命令：sudo service named start 啟動。
注意：如果啟動時報錯說找不到named.conf文件，可以手動新建一個空白的namd.conf文件，再試下使用sudo service named start 命令啟動。
⑶ 怎麼由namd所的dcd文件做sdf
1、將SQLServer Compact 3.5 安裝目錄下的如下文件復制到將要打包發布的項目中 sqlceca35.dll sqlcecompact35.dll sqlceer35EN.dll sqlceme35.dll sqlceoledb35.dll sqlceqp35.dll sqlcese35.dll 2、將這些文件的「復制到輸出目錄」屬性設置為「如..
⑷ 如何用gromacs分析namd的軌跡
GROMACS計算MMPBSA
eming
AMBER有一套可以計算MMPBSA的程序，像NAMD或者GROMACS也有一幫人喜歡給寫個類似的程序，譬如PBSA的計算採用APBS，原理是行的通的，於是NAMD下就有iAPBS的程序（http://mccammon.ucsd.e/iapbs/），GROMACS下也有，
參見及下載g_mmpbsa
http:
程序安裝：
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
這個在Gromacs和APBS編譯之後是有的。APBS里能用OpenMP進行並行計算，通過環境變數控制使用的核/處理器數目，
export OMP_NUM_THREADS=X
Installation1.
Configure to install
To 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
詳細用法請參見
http://rashmikumari.github.io/g_mmpbsa/Usage.html#g_mmpbsa
除了自己編譯以外，官方網站現在已經提供已經編譯好的執行文件，需要的話可以直接下載http:/
g_mmpbsa
g_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 givesresie wise contribution to total binding energy which will provideinformation about important contributing resies 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 resieper frame/snaspshot.
-pcon contrib_pol.dat
Polarsolvation energy contribution per resie frame wise.
-apcon contrib_apol.dat
Non-polarsolvation energy contribution per resie 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 resie to total binding energy willbe calculated using energy decomposition scheme.
---------------------------編譯過程-----------------------------
g_mmpbsa的下載：
http://rashmikumari.github.io/g_mmpbsa/
--------compiling-Gromacs-4.5.5--------
GROMACS需要生成靜態庫編譯
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,所以請下載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--------------
同樣下載壓縮包，解壓後編譯
./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的編譯, 如果環境變數含有ifort,它會自動選擇用intel的ifort來編譯，這樣g_mmpbsa也應當使用ifort來編譯.或者強制apbs採用gfortran等來編譯。
如此以來也可以將NAMD的軌跡轉換為gromacs的軌跡來計算MMPBSA。
拓撲文件可以使用psf2top.py來執行;
軌跡文件可以用mdconvert或者wordom來轉換
Amber的拓撲文件/結構文件可以用acpype來轉換
-----------------
還是強調如果自己不想編譯；直接從官網站下載預編譯好的就可以了。