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yalefield

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[资源] 【分享】MM/PBSA

看gwdavid着急得很，http://muchong.com/bbs/viewthread.php?tid=1097215
老汉只好亲自......转贴

动力学分析方法多种多样，但是能量永远是不变的话题，很多问题的说明都是以能量为基础的，这里说的能量包括各种力场能量，溶剂化能，自由能等。

在amber中，可以通过mmpbsa来计算这个相对自由能。
在免费的软件gromacs中，能量计算相当粗糙，虽然提供了计算自由能的工具，但是源码中却是空，不知道到哪个版本才能实现。
GROMACS 4.0应该有所动作了吧

amber是比较好用，但是也是一个收费软件，特别是想发文章的朋友要注意了。如果是不想买amber的朋友，中间路线：

用gromacs跑轨迹
用autodock算能量（自由能）
虽然不如mmpbsa原理上准确，但是忽略部分熵效应也在变动不大的体系也还不错。

[ Last edited by mingdong on 2009-6-25 at 15:52 ]

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1楼 2008-12-12 18:34:17

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yalefield

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GROMACS

★ ★ ★ ★
fegg7502(金币+4,VIP+0):thank you very much! 12-6 18:29

Tips for MM/PBSA calculations

This section provides some hints on how to use the tools you've already learned about in this class to perform MM/PBSA calculations on your systems.

Additionally, it is assumed (or hoped) that you are able to write scripts in some language since that will simplify many of the repetitive tasks listed here.

Generating PQR files

This section assumes that you've generated one (or more) PDB files from your GROMACS-format trajectory. However, you'll need to do a bit of post-processing to make the nomenclature used by GROMACS consistent with the PARSE force field (see below). This can be accomplished by applying the following sed commands to each PDB file produced by GROMACS:

$ cat in.pdb | sed -e "s/PRO A 1/PR+ A 1/g" | sed -e "s/PRO B 100/PR+ B 100/g" > out.pdb

You've already learned how to transform PDB files into PQR in the pKa section of the class. However, those files contained only standard amino acids; the files we're interested in contain the non-standard amprenavir drug. Therefore, we'll be using a custom command-line version of PDB2PQR for this class.

If you set your path correctly earlier, you should be able to type pdb2pqr.py and get a basic help screen. More detailed documentation is available from the PDB2PQR home page(http://pdb2pqr.sf.net/).

As mentioned above, we have installed a specialized version of PDB2PQR with amprenavir parameters. However, these parameters are only available with the PARSE force field[1]. Therefore, you will need to invoke PDB2PQR with the PARSE force field. We will also not be using any of the hydrogen rebuilding methods. Therefore, in general, you will invoke PDB2PQR as

$ pdb2pqr.py --assign-only --ff=parse input.pdb output.pqr

where input.pdb is the input PDB file and output.pqr is the output PQR.

It's probably worthwhile to use the --apbs-input option with one of your PDB files to generate input for the APBS solvation energy calculations.

Notes

More details on this force field are available in the original paper:

Sitkoff D, Sharp KA, Honig B.
Accurate calculation of hydration free energies using macroscopic solvent models.
Journal of Physical Chemistry. 98 (7), 1978-88, 1994.
http://pubs.acs.org/cgi-bin/samp ... pdf/j100058a043.pdf

[ Last edited by yalefield on 2008-12-12 at 18:38 ]

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2楼2008-12-12 18:37:06

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yalefield

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AutoDock

★ ★ ★ ★
fegg7502(金币+4,VIP+0):thank you very much! 12-6 18:30

下面这个脚本可以实现这一功能：

#!/bin/sh
#'$1' is set for different list name
#'$2' is set for the ligand name #prepare the $2.bnd in advance with command:

#/

~root/autodock/dist305/bin/pdbtoatm lig.pdbq|

~root/autodock/dist305/bin/atmtobnd >lig.bnd for snapshot in `cat $1`
do rec=protein_mn_hoh1.${snapshot} lig=$2.${snapshot} echo ${rec}

#assign the atomic solvation parameters to PDBQ-formatted version of your macromolecule,
~root/bin/addsol ${rec}.pdbq ${rec}.pdbqs
~root//bin/autotors -A $2.bnd ${lig}.pdbq ${lig}.out.pdbq > ${lig}.out.${rec}.epdb.com
~root/autodock/dist305/bin/autodock3 -p ${lig}.out.${rec}.dpf -l ${lig}.out.${rec}.epdb.log -c > $1_Binding
~root//bin/Docked.awk ${lig}.out.${rec}.epdb.log >> $1_Docked
~root//bin/Inter_score.awk ${lig}.out.${rec}.epdb.log >> $1_Inter_Energy
~root//bin/Intra_score.awk ${lig}.out.${rec}.epdb.log >> $1_Intra_Energy #rm -f *.map *.fld *.xyz *.err *.pdbqs *.glg *.log *.com *.gpf *.dpf
Binding.awk

#!
~root/bin/gawk -f BEGIN{ name=ARGV[1] split(name,array,"."

}
{
if($0 ~ /Estimated Free Energy of Binding/)
{
print array[1]" "$9" " $10
}
}

Docked.awk

#!~root/bin/gawk -f BEGIN{ name=ARGV[1] split(name,array,"."

}
{
if($0 ~ /Final Docked Energy/) {print array[1]" "$7" " $8}
}

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3楼2008-12-12 18:43:44

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖