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小木虫论坛-学术科研互动平台 » 计算模拟区 » 分子模拟 » Gromacs/Amber/NAMD » 求Gromacs中Glycam力场数据包。。非常感谢
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陈应广

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[求助] 求Gromacs中Glycam力场数据包。。非常感谢

本人最近在研究糖蛋白的模拟，做出pdb结构文件后，找不到合适的力场，查资料只有Glycam力场适合，但又苦于自己是个新手，寻找不到力场数据包。。还望哪位好心人给传一份吧？？非常感谢！！

[ Last edited by ben_ladeng on 2011-12-22 at 19:03 ]
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1楼 2011-12-19 14:24:18
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shengxiang

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【答案】应助回帖

★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
御剑江湖(金币+3): EPI鼓励原创，此解答在分子模拟论坛已有，http://www.mdbbs.org/thread-215-1-1.html 2011-12-21 18:40:01
陈应广(金币+8): ★★★很有帮助 谢谢您的帮助！ 2011-12-22 09:34:23
jiaoyixiong(金币+10, 模拟EPI+1): 鼓励交流 2011-12-22 14:11:05
gromacs中添加amber力场有两种方法：(1)从http://ffamber.cnsm.csulb.edu/上下载对应于你的gromacs版本的amber力场参数文件，具体的步骤如下：
Installation & Testing:
(1) Install the desired GROMACS distribution (v3.1.4, v3.2.1, v3.3, or v3.3.1).
(2) Download the appropriate ffamber ports (.tar.gz) with or without pdf documentation from the table below, being sure that the version number you choose matches the version of GROMACS you are using.
(3) Unzip/untar the downloaded tar.gz file.
(4) Copy aminoacids.dat and vdwradii.dat to the "top" directory in your gromacs distribution (you should see force field files there, such as ffoplsaa.*). If you plan on simulating nucleic acids, refer to the note for nucleic acids in aminoacids.dat below.
(5) Files for each force field are located in a seperate subdirectory, such as ffamber94/ for the Cornell potential. Copy the desired ffamber* files to the top directory in your gromacs distribution.
(6) Increment the number at the top of the "top/FF.dat" file by 1 for each AMBER port you'll install (so that it matches the total number of forcefields available in the "top" directory).
(7) Add lines like the following to the "top/FF.dat" file. These are used by pdb2gmx to allow you to identify the desired FF and field 1 must match the ffamber* filename prefixes, whereas the following fields can be user-defined:
     ffamber94 AMBER94 Cornell protein/nucleic forcefield
     ffamber99 AMBER99 Wang protein/nucleic acid forcefield
     ffamber99p AMBER99p protein/nucleic forcefield
     ffamber03 AMBER03 Duan protein/nucleic forcefield
(8) Locate the GMXRC in your GROMACS distribution and run `source GMXRC`.
(9) Run `pdb2gmx -H14 -f any.pdb` with any pdb to verify that these force fields are now seen by GROMACS. Working example .pdb files are available below, alongside pre-prepared gro and top files (GROMACS 3.1.4 / AMBER94) to which you can compare your resulting files.
(2).你可以编译高版本的gromacs，例如4.5，里面自带了amber力场，免去了另外安装的麻烦~
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5楼2011-12-21 18:35:56
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陈应广

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我的邮箱：cygazy@163.com
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2楼2011-12-19 14:25:43
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shengxiang

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【答案】应助回帖

★ ★
感谢参与，应助指数 +1
陈应广(金币+2): ★有帮助 谢谢您的帮助！我主要是想要一份能在Gromacs里运行的Glycam数据包，哪位好心人帮忙给传一份？ 2011-12-21 09:14:34
御剑江湖(金币+2): 谢谢 2011-12-21 18:44:15
http://www.pharmacy.manchester.ac.uk/bryce/amber
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3楼2011-12-21 08:54:51
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陈应广

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引用回帖:
楼: Originally posted by shengxiang at 2011-12-21 08:54:51:
http://www.pharmacy.manchester.ac.uk/bryce/amber

您好，请问你那里有能在Gromacs里运行的Glycam力场数据包吗？？能否教教小弟怎么在Gromacs里添加Amber力场？？
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4楼2011-12-21 09:18:23
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shengxiang

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★ ★ ★ ★
御剑江湖(金币+4): 同一解答不得多少授予EPIO,http://emuch.net/bbs/viewthread.php?tid=3959648&page=1#pid5 2011-12-22 14:56:10
gromacs中添加amber力场有两种方法：
(1)从http://ffamber.cnsm.csulb.edu/上下载对应于你的gromacs版本的amber力场参数文件，具体的步骤如下：
Installation & Testing:
(1) Install the desired GROMACS distribution (v3.1.4, v3.2.1, v3.3, or v3.3.1).
(2) Download the appropriate ffamber ports (.tar.gz) with or without pdf documentation from the table below, being sure that the version number you choose matches the version of GROMACS you are using.
(3) Unzip/untar the downloaded tar.gz file.
(4) Copy aminoacids.dat and vdwradii.dat to the "top" directory in your gromacs distribution (you should see force field files there, such as ffoplsaa.*). If you plan on simulating nucleic acids, refer to the note for nucleic acids in aminoacids.dat below.
(5) Files for each force field are located in a seperate subdirectory, such as ffamber94/ for the Cornell potential. Copy the desired ffamber* files to the top directory in your gromacs distribution.
(6) Increment the number at the top of the "top/FF.dat" file by 1 for each AMBER port you'll install (so that it matches the total number of forcefields available in the "top" directory).
(7) Add lines like the following to the "top/FF.dat" file. These are used by pdb2gmx to allow you to identify the desired FF and field 1 must match the ffamber* filename prefixes, whereas the following fields can be user-defined:
     ffamber94 AMBER94 Cornell protein/nucleic forcefield
     ffamber99 AMBER99 Wang protein/nucleic acid forcefield
     ffamber99p AMBER99p protein/nucleic forcefield
     ffamber03 AMBER03 Duan protein/nucleic forcefield
(8) Locate the GMXRC in your GROMACS distribution and run `source GMXRC`.
(9) Run `pdb2gmx -H14 -f any.pdb` with any pdb to verify that these force fields are now seen by GROMACS. Working example .pdb files are available below, alongside pre-prepared gro and top files (GROMACS 3.1.4 / AMBER94) to which you can compare your resulting files.
翻译如下：
1.安装gromacs并确定你的gromacs的版本；
2.从http://ffamber.cnsm.csulb.edu/上下载对应于你的gromacs版本的amber力场参数文件；
3.解压缩下载的amber力场参数文件（linux下：tar –zxvf  ***）；
4.复制aminoacids.dat和vdwradii.dat到gromacs的top文件夹下；
5.每一个力场文件都在一个单独的子文件夹中，复制所需要的ffamber的文件夹下所有文件到top文件夹下；
6.增加“top/FF.dat”中力场的数目，每添加一个力场增加1；
7.增加link到“otop/FF.dat”中，格式如下：
ffamber94 AMBER94 Cornell protein/nucleic forcefield
ffamber99 AMBER99 Wang protein/nucleic acid forcefield
ffamber99p AMBER99p protein/nucleic forcefield
ffamber03 AMBER03 Duan protein/nucleic forcefield；
8.找到gromacs中的GMXRC并且“source GMXRC”；
9.运行“pdb2gmx –f **.pdb –o **.gro –p **.top”进行测试。
(2).你可以编译高版本的gromacs，例如4.5，里面自带了amber力场，免去了另外安装的麻烦~
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6楼2011-12-22 12:53:10
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