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: 3666  |  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

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+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

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
[基金申请] 人气不行了 +11 fansofjerry 2026-08-21 11/550 2026-08-25 11:04 by 孤独的英雄6
[基金申请] 2026国自然函评费到账 +19 羊腰板 2026-08-21 22/1100 2026-08-25 10:38 by popular289
[教师之家] 导师吐槽：我怎么摊上了这么个极品研究生！ +3 苏东坡二世 2026-08-23 3/150 2026-08-25 10:35 by shisan1313
[基金申请] 2026年的国家社科基金项目通讯评审的新规则与新动向、新挑战 +5 process2012 2026-08-23 7/350 2026-08-25 09:42 by huixian257
[基金申请] 范进中举一文的中心思想 +7 炎黄贵胄 2026-08-22 8/400 2026-08-25 08:48 by ZJTJZ
[基金申请] 如果此刻你正在为国基感到焦虑，不妨来听听这首《基金之外》 +7 scalable 2026-08-24 7/350 2026-08-24 23:01 by anata1209
[基金申请] 没有任何消息-是不是就凉了 +7 图啦图啦 2026-08-24 8/400 2026-08-24 22:00 by maomao_da
[基金申请] 能否退出参与的面上项目解除限项 +21 koalala 2026-08-24 24/1200 2026-08-24 19:25 by 家与远方
[基金申请] filecode，4个jtjc了 +14 ziyangfang 2026-08-19 17/850 2026-08-24 18:37 by 哈哈蛤？
[基金申请] 建议基金发布提前给出明确的时间点 +13 kulium 2026-08-21 16/800 2026-08-24 16:27 by superceng
[基金申请] 今日不放榜？网传国自然预计 8 月 27 日可查结果 +17 医学老男孩 2026-08-20 21/1050 2026-08-24 14:21 by refreshing11
[基金申请] 估计是周四 +4 archvillain 2026-08-18 4/200 2026-08-24 13:53 by zzuzxg
[基金申请] 放榜前的不淡定 20+4 snowwithsea 2026-08-19 17/850 2026-08-24 10:20 by echo8914667
[基金申请] 什么时候开奖？ +10 CrisMessi 2026-08-18 11/550 2026-08-24 06:50 by 开心的小狮子
[教师之家] 跳槽后在研项目怎么办？ +5 简单化xn 2026-08-22 10/500 2026-08-23 12:38 by 简单化xn
[基金申请] 今天放榜吗？ +15 布布和一二 2026-08-19 16/800 2026-08-23 09:55 by 张春生
[基金申请] 时间戳又变了 +13 wuchongjun 2026-08-20 19/950 2026-08-21 17:21 by 紫杉醇
[基金申请] 今天放榜没戏了吧 +9 yuleib84 2026-08-19 11/550 2026-08-21 10:06 by gltch
[基金申请] 基金啊基金 +4 longfie172 2026-08-20 4/200 2026-08-21 08:58 by mark mao
[基金申请] 重要消息，中午系统在维护 +11 yuleib84 2026-08-18 12/600 2026-08-20 11:09 by xskun
信息提示
关闭
请填处理意见
关闭