应《网络安全法》要求，自2017年10月1日起，未进行实名认证将不得使用互联网跟帖服务。为保障您的帐号能够正常使用，请尽快对帐号进行手机号验证，感谢您的理解与支持！

24小时热门版块排行榜    

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
61/1返回列表
查看: 3334  |  回复: 5
只看楼主 @他人 存档 新回复提醒 (忽略) 收藏    在APP中查看
本帖产生 1 个 模拟EPI ，点击这里进行查看

陈应广

新虫 (初入文坛)

[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 ]
回复此楼

» 收录本帖的淘帖专辑推荐

gromacs 力场

» 猜你喜欢

» 本主题相关价值贴推荐，对您同样有帮助:
1楼 2011-12-19 14:24:18
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖
回帖置顶 ( 共有1个 )

shengxiang

木虫 (著名写手)

【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~
赞一下(2人) 回复此楼
5楼2011-12-21 18:35:56
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖
普通回帖

陈应广

新虫 (初入文坛)
我的邮箱：cygazy@163.com
赞一下 回复此楼
2楼2011-12-19 14:25:43
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

shengxiang

木虫 (著名写手)

【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
赞一下(1人) 回复此楼
3楼2011-12-21 08:54:51
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

陈应广

新虫 (初入文坛)
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？？
赞一下 回复此楼
4楼2011-12-21 09:18:23
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖

shengxiang

木虫 (著名写手)

【答案】应助回帖

★ ★ ★ ★
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~
赞一下(1人) 回复此楼
6楼2011-12-22 12:53:10
已阅   回复此楼   关注TA 给TA发消息 送TA红花 TA的回帖
相关版块跳转 我要订阅楼主 陈应广 的主题更新
61/1返回列表
普通表情 龙 兔 虎 猫
最具人气热帖推荐 [查看全部] 作者 回/看 最后发表
[考博] 东华理工大学化材专业26届硕士博士申请 +6 zlingli 2026-03-13 6/300 2026-03-15 20:00 by ryzcf
[考研] 中科大材料与化工319求调剂 +3 孟鑫材料 2026-03-14 3/150 2026-03-14 20:10 by ms629
[考研] 中科大材料专硕319求调剂 +3 孟鑫材料 2026-03-13 3/150 2026-03-14 18:10 by houyaoxu
[考研] 复试调剂 +4 z1z2z3879 2026-03-14 5/250 2026-03-14 16:30 by JourneyLucky
[考研] 一志愿哈工大材料324分求调剂 +5 闫旭东 2026-03-14 5/250 2026-03-14 14:53 by 木瓜膏
[考研] 267一志愿南京工业大学0817化工求调剂 +5 SUICHILD 2026-03-12 5/250 2026-03-14 14:53 by jean5056
[考研] 290求调剂 +4 @将就将就看 2026-03-10 8/400 2026-03-14 14:23 by 千千运气
[考研] 材料080500调剂求收留 +3 一颗meteor 2026-03-13 3/150 2026-03-14 10:54 by peike
[考研] b区环境工程求调剂 +4 Maps1 2026-03-10 6/300 2026-03-14 00:23 by JourneyLucky
[考研] 2026考研调剂+本科延边大学+山东大学+生物化学与分子生物学+有项目经验 +3 ccdsscjy 2026-03-10 3/150 2026-03-14 00:12 by JourneyLucky
[考研] 332求调剂 +3 zjy101327 2026-03-11 6/300 2026-03-13 22:48 by JourneyLucky
[考研] 311求调剂 +3 冬十三 2026-03-13 3/150 2026-03-13 20:41 by JourneyLucky
[硕博家园] 085600 260分求调剂 +3 天空还下雨么 2026-03-13 5/250 2026-03-13 18:46 by 天空还下雨么
[硕博家园] 深圳大学硕士招生（2026秋，传感器方向，仅录取第一志愿） +4 xujiaoszu 2026-03-11 7/350 2026-03-13 17:28 by xujiaoszu
[考研] 求调剂 +7 18880831720 2026-03-11 7/350 2026-03-13 16:10 by JourneyLucky
[考研] 268求调剂 +4 好运连绵不绝 2026-03-12 4/200 2026-03-13 10:45 by hyswxzs
[考研] 材料专硕274一志愿陕西师范大学求调剂 +4 薛云鹏 2026-03-13 4/200 2026-03-13 10:40 by 学员8dgXkO
[考研] 工科0856专硕化学工程269能调剂吗 +10 我想读研11 2026-03-10 10/500 2026-03-13 10:14 by Yuyi.
[考研] 0856材料与化工353分求调剂 +11 NIFFFfff 2026-03-09 11/550 2026-03-10 18:36 by suyuanhai
[考研] 085602化工求调剂 +7 董boxing 2026-03-10 7/350 2026-03-10 17:07 by BruceLiu320
信息提示
关闭
请填处理意见
关闭