 |
 |
 |
 |
 |
 |
||
 |
 |
 |
 |
 |
| 3 | 1/1 | 返回列表 |
| 查看: 1100 | 回復(fù): 2 | |||
[交流]
在計算能量分解時存在的問題，希望大家能共同探討一下
|
|
我用軟件是amber10 這是報錯信息： [amber@localhost binding-famo]$ mm_pbsa.pl binding.in > binding.out /usr/local/amber10/exe/sander -O -i sander_com.in -o sander_com.1.out -c ../snapshot/complex_com.crd.1 -p ../com.prmtop not successful 輸出文件如下： =>> Init data Presuming executables of amber suite to be in /usr/local/amber10/exe =>> Reading input parameters Found PREFIX => complex Found PATH => ../snapshot/ Found COMPLEX => 1 Found RECEPTOR => 1 Found LIGAND => 1 Found COMPT => ../com.prmtop Found RECPT => ../rec.prmtop Found LIGPT => ../lig.prmtop Found GC => 0 Found AS => 0 Found DC => 0 Found MM => 1 Found GB => 1 Found PB => 1 Found MS => 1 Found NM => 0 Found PROC => 2 Found REFE => 0 Found INDI => 1.0 Found EXDI => 80.0 Found SCALE => 2 Found LINIT => 1000 Found PRBRAD => 1.4 Found ISTRNG => 0.0 Found RADIOPT => 0 Found NPOPT => 1 Found CAVITY_SURFTEN => 0.0072 Found CAVITY_OFFSET => 0.00 Found SURFTEN => 0.0072 Found SURFOFF => 0.00 Found DIELC => 1.0 Found IGB => 2 Found GBSA => 1 Found SALTCON => 0.00 Found EXTDIEL => 80.0 Found INTDIEL => 1.0 Found SURFTEN => 0.0072 Found SURFOFF => 0.00 Found PROBE => 0.0 =>> Checking sanity Checking GENERAL Setting START to default 1 Setting STOP to default 10e10 Setting OFFSET to default 1 Setting VERBOSE to default 0 Checking MM Checking PB Checking GB Checking MS =>> Creating input Sander input PBSA input =>> Calculating energy / entropy contributions Calc contrib for ../snapshot/complex_com.crd.1 Calc MM/GB/SAS 結(jié)合能計算的腳本如下： Input parameters for mm_pbsa.pl # # Holger Gohlke # 08.01.2002 # ################################################################################ @GENERAL # # General parameters # 0: means NO; >0: means YES # # mm_pbsa allows to calculate (absolute) free energies for one molecular # species or a free energy difference according to: # # Receptor + Ligand = Complex, # DeltaG = G(Complex) - G(Receptor) - G(Ligand). # # PREFIX - To the prefix, "{_com, _rec, _lig}.crd.Number" is added during # generation of snapshots as well as during mm_pbsa calculations. # PATH - Specifies the location where to store or get snapshots. # # COMPLEX - Set to 1 if free energy difference is calculated. # RECEPTOR - Set to 1 if either (absolute) free energy or free energy # difference are calculated. # LIGAND - Set to 1 if free energy difference is calculated. # # COMPT - parmtop file for the complex (not necessary for option GC). # RECPT - parmtop file for the receptor (not necessary for option GC). # LIGPT - parmtop file for the ligand (not necessary for option GC). # # GC - Snapshots are generated from trajectories (see below). # AS - Residues are mutated during generation of snapshots from trajectories. # DC - Decompose the free energies into individual contributions # (only works with MM and GB). # # MM - Calculation of gas phase energies using sander. # GB - Calculation of desolvation free energies using the GB models in sander # (see below). # PB - Calculation of desolvation free energies using delphi (see below). # Calculation of nonpolar solvation free energies according to # the NPOPT option in pbsa (see below). # MS - Calculation of nonpolar contributions to desolvation using molsurf # (see below). # If MS == 0 and GB == 1, nonpolar contributions are calculated with the # LCPO method in sander. # If MS == 0 and PB == 1, nonpolar contributions are calculated according # the NPOPT option in pbsa (see below). # NM - Calculation of entropies with nmode. # PREFIX complex PATH ../snapshot/ # COMPLEX 1 RECEPTOR 1 LIGAND 1 # COMPT ../com.prmtop RECPT ../rec.prmtop LIGPT ../lig.prmtop # GC 0 AS 0 DC 0 # MM 1 GB 1 PB 1 MS 1 # NM 0 # ################################################################################ @PB # # PB parameters (this section is only relevant if PB = 1 above) # # The following parameters are passed to the PB solver. # Additional input parameters may also be added here. See the sander PB # documentation for more options. # # PROC - Determines which method is used for solving the PB equation: # By default, PROC = 2, the pbsa program of the AMBER suite is used. # REFE - Determines which reference state is taken for PB calc: # By default, REFE = 0, reaction field energy is calculated with # EXDI/INDI. Here, INDI must agree with DIELC from MM part. # INDI - Dielectric constant for the solute. # EXDI - Dielectric constant for the surrounding solvent. # ISTRNG - Ionic strength (in mM) for the Poisson-Boltzmann solvent. # PRBRAD - Solvent probe radius in Angstrom: # 1.4: with the radii in the prmtop files. Default. # 1.6: with the radii optimized by Tan and Luo (In preparation). # See RADIOPT on how to choose a cavity radii set. # RADIOPT - Option to set up radii for PB calc: # 0: uses the radii from the prmtop file. Default. # 1: uses the radii optimized by Tan and Luo (In preparation) # with respect to the reaction field energies computed # in the TIP3P explicit solvents. Note that optimized radii # are based on AMBER atom types (upper case) and charges. # Radii from the prmtop files are used if the atom types # are defined by antechamber (lower case). # SCALE - Lattice spacing in no. of grids per Angstrom. # LINIT - No. of iterations with linear PB equation. # # NP Parameters for nonpolar solvation energies if MS = 0 # # NPOPT - Option for modeling nonpolar solvation free energy. # See sander PB documentation for more information on the # implementations by Tan and Luo (In preparation). # 1: uses the solvent-accessible-surface area to correlate total # nonpolar solvation free energy: # Gnp = CAVITY_SURFTEN * SASA + CAVITY_OFFSET. Default. # 2: uses the solvent-accessible-surface area to correlate the # repulsive (cavity) term only, and uses a surface-integration # approach to compute the attractive (dispersion) term: # Gnp = Gdisp + Gcavity # = Gdisp + CAVITY_SURFTEN * SASA + CAVITY_OFFSET. # When this option is used, RADIOPT has to be set to 1, # i.e. the radii set optimized by Tan and Luo to mimic Gnp # in TIP3P explicit solvents. Otherwise, there is no guarantee # that Gnp matches that in explicit solvents. # CAVITY_SURFTEN/CAVITY_OFFSET - Values used to compute the nonpolar # solvation free energy Gnp according NPOPT. The default values # are for NPOPT set to 0 and RADIOPT set to 0 (see above). # If NPOPT is set to 1 and RADIOPT set to 1, these two lines # can be removed, i.e. use the default values set in pbsa # for this nonpolar solvation model. Otherwise, please # set these to the following: # CAVITY_SURFTEN: 0.04356 # CAVITY_OFFSET: -1.008 # # NP Parameters for nonpolar solvation energies if MS = 1 # # SURFTEN/SURFOFF - Values used to compute the nonpolar contribution Gnp to # the desolvation according to Gnp = SURFTEN * SASA + SURFOFF. # PROC 2 REFE 0 INDI 1.0 EXDI 80.0 SCALE 2 LINIT 1000 PRBRAD 1.4 ISTRNG 0.0 RADIOPT 0 NPOPT 1 CAVITY_SURFTEN 0.0072 CAVITY_OFFSET 0.00 # SURFTEN 0.0072 SURFOFF 0.00 # ################################################################################ @MM # # MM parameters (this section is only relevant if MM = 1 above) # # The following parameters are passed to sander. # For further details see the sander documentation. # # DIELC - Dielectricity constant for electrostatic interactions. # Note: This is not related to GB calculations. # DIELC 1.0 # ################################################################################ @GB # # GB parameters (this section is only relevant if GB = 1 above) # # The first group of the following parameters are passed to sander. # For further details see the sander documentation. # # IGB - Switches between Tsui's GB (1), Onufriev's GB (2, 5). # GBSA - Switches between LCPO (1) and ICOSA (2) method for SASA calc. # Decomposition only works with ICOSA. # SALTCON - Concentration (in M) of 1-1 mobile counterions in solution. # EXTDIEL - Dielectricity constant for the solvent. # INTDIEL - Dielectricity constant for the solute # # SURFTEN / SURFOFF - Values used to compute the nonpolar contribution Gnp to # the desolvation according to Gnp = SURFTEN * SASA + SURFOFF. # IGB 2 GBSA 1 SALTCON 0.00 EXTDIEL 80.0 INTDIEL 1.0 # SURFTEN 0.0072 SURFOFF 0.00 # ################################################################################ @MS # # Molsurf parameters (this section is only relevant if MS = 1 above) # # PROBE - Radius of the probe sphere used to calculate the SAS. # Since Bondi radii are already augmented by 1.4A, PROBE should be 0.0 # PROBE 0.0 # ################################################################################# @PROGRAMS # # Additional program executables can be defined here |
回復(fù)此樓» 猜你喜歡
求材料調(diào)劑
已經(jīng)有7人回復(fù)
-
一志愿天大材料與化工（085600）總分338
已經(jīng)有3人回復(fù)
-
085600材料與化工
已經(jīng)有5人回復(fù)
-
085600材料與化工調(diào)劑 324分
已經(jīng)有6人回復(fù)
-
286求調(diào)劑
已經(jīng)有9人回復(fù)
-
焦慮
已經(jīng)有12人回復(fù)
-
344求調(diào)劑
已經(jīng)有6人回復(fù)
-
266求調(diào)劑
已經(jīng)有9人回復(fù)
-
化學(xué)工程321分求調(diào)劑
已經(jīng)有18人回復(fù)
-
314求調(diào)劑
已經(jīng)有8人回復(fù)
» 本主題相關(guān)價值貼推薦，對您同樣有幫助:
- 大家?guī)兔匆幌拢珹DF計算帶有未成對電子體系的能量分解分析
已經(jīng)有3人回復(fù)
- 數(shù)學(xué)青年基金,手工僅查出9個!
已經(jīng)有55人回復(fù)
- 【討論】討論一下，用ms計算系統(tǒng)能量問題
已經(jīng)有4人回復(fù)
- 【轉(zhuǎn)帖】理解矩陣
已經(jīng)有51人回復(fù)
» 搶金幣啦！回帖就可以得到:
-
青島高校2026招生碩士研究生
+5/855
-
山東征女友，坐標(biāo)濟(jì)南
+1/167
-
散金幣，求好運，祝面上順利！
+2/102
-
化學(xué)化工學(xué)院 招收化工、化學(xué)、材料等相關(guān)方向研究生（學(xué)碩、專碩都有調(diào)劑名額）
+1/96
-
物理學(xué) 調(diào)劑
+1/84
-
光學(xué)工程學(xué)碩調(diào)劑信息
+2/46
-
2026年重慶工商大學(xué)管理科學(xué)與工程專業(yè)學(xué)術(shù)碩士招生調(diào)劑，風(fēng)景總在柳暗花明處
+1/36
-
湘潭大學(xué)“過程強(qiáng)化與綠色化工”創(chuàng)新團(tuán)隊補(bǔ)招2026年秋入學(xué)博士生
+1/35
-
中國科學(xué)院杭州醫(yī)學(xué)研究所覃江江課題組招聘博士后
+1/35
-
新加坡國立大學(xué)藥學(xué)系化學(xué)生物學(xué)課題組招PhD
+1/16
-
211/雙一流---石河子大學(xué)---有機(jī)化學(xué)方向招調(diào)劑生
+1/16
-
國家級領(lǐng)軍人才團(tuán)隊高分子材料方向2026年博士研究生招生
+1/15
-
南開大學(xué)羅景山教授課題組招收2026年入學(xué)博士生（光/電催化方向）
+2/14
-
南京醫(yī)科大學(xué)-膜蛋白結(jié)構(gòu)與功能課題組-招收2026級博士研究生
+1/11
-
南昌航空大學(xué)代威力教授招收光催化和光熱催化研究方向博士生
+1/9
-
【博士招生】武漢科技大學(xué)招收材料、化工、環(huán)境、冶金類2026年“申請-考核”制博士生
+1/8
-
課題組招收環(huán)境及相關(guān)專業(yè)調(diào)劑碩士研究生（歡迎優(yōu)秀學(xué)生加入）
+1/6
-
論文投出，祈福，求好運
+1/3
-
深圳大學(xué)蔡興科課題組博士后及研究助理招聘
+1/2
-
Top-88悉尼科技大學(xué)數(shù)據(jù)科學(xué)/AI 招收2027年入學(xué) 校獎 博士生1到2名(國際和本地學(xué)生）
+1/2
2樓2012-03-24 09:56:57
3樓2016-04-07 09:08:17
相關(guān)版塊跳轉(zhuǎn)
我要訂閱樓主 落雁雙飛 的主題更新
| 3 | 1/1 | 返回列表 |
| 最具人氣熱帖推薦 [查看全部] | 作者 | 回/看 | 最后發(fā)表 | |
|---|---|---|---|---|
|
[考研] 296求調(diào)劑 +5 | 大口吃飯 身體健 2026-03-13 | 5/250 |
|
|---|---|---|---|---|
|
|
[考研] 277調(diào)劑 +5 | 自由煎餅果子 2026-03-16 | 6/300 |
|
|
|
[考研] 268求調(diào)劑 +8 | 一定有學(xué)上- 2026-03-14 | 9/450 |
|
|
|
[考研] 一志愿蘇州大學(xué)材料工程（085601）專碩有科研經(jīng)歷三項國獎兩個實用型專利一項省級立項 +6 | 大火山小火山 2026-03-16 | 8/400 |
|
|
[考研] 考研調(diào)劑 +3 | 淇ya_~ 2026-03-17 | 5/250 |
|
|
|
[考研] 274求調(diào)劑 +5 | 時間點 2026-03-13 | 5/250 |
|
|
|
[考研] 機(jī)械專碩325，尋找調(diào)劑院校 +3 | y9999 2026-03-15 | 5/250 |
|
|
|
[考研] 085600調(diào)劑 +5 | 漾漾123sun 2026-03-12 | 6/300 |
|
|
|
[考研] 070303一志愿西北大學(xué)學(xué)碩310找調(diào)劑 +5 | d如愿上岸 2026-03-12 | 8/400 |
|
|
|
[考研]
 機(jī)械專碩調(diào)劑
+3
|
笨笨兔子 2026-03-12 | 3/150 |
|
|
|
[考研] 26考研一志愿中國石油大學(xué)(華東)305分求調(diào)劑 +3 | 嘉年新程 2026-03-15 | 3/150 |
|
|
|
[考研] 22408總分284求調(diào)劑 +3 | InAspic 2026-03-13 | 3/150 |
|
|
|
[考研] 085601材料工程315分求調(diào)劑 +3 | yang_0104 2026-03-15 | 3/150 |
|
|
|
[考研] 080500，材料學(xué)碩302分求調(diào)劑學(xué)校 +4 | 初識可樂 2026-03-14 | 5/250 |
|
|
|
[考研] 材料工程327求調(diào)劑 +3 | xiaohe12w 2026-03-11 | 3/150 |
|
|
|
[考研] 本科南京大學(xué)一志愿川大藥學(xué)327 +3 | 麥田耕者 2026-03-14 | 3/150 |
|
|
|
[考研] 328求調(diào)劑 +3 | 5201314Lsy！ 2026-03-13 | 6/300 |
|
|
|
[考研] 考研調(diào)劑 +4 | 芬達(dá)46 2026-03-12 | 4/200 |
|
|
|
[考研] 307求調(diào)劑 +5 | 超級伊昂大王 2026-03-12 | 5/250 |
|
|
|
[考研] 一志愿211化學(xué)學(xué)碩310分求調(diào)劑 +8 | 努力奮斗112 2026-03-12 | 9/450 |
|