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标题: amber 调用不了guassian09 的问题 [打印本页]
作者Author: hhhnano 时间: 2019-12-22 11:17
标题: amber 调用不了guassian09 的问题
按照sob老师的教程先在笔记本电脑上安装了gaussian E01, gview, 也安装了Amber12
http://bbs.keinsci.com/thread-10814-1-1.html
gview ，g09运行正常，
Entering Gaussian System, Link 0=g09
安装和配置具体步骤：
unzipgaosi09-E01.zip
mkdir/home/xzhfood/gaussian/g09/scratch
su
cdgaussian
chmod750 -R *
cdg09
chmod 775 -R scratch
查看文件权限
stat -c '%A %a %n' *
配置：
gedit/home/xzhfood/.bashrc
#gaussian09
exportg09root=/home/xzhfood/gaussian
exportGAUSS_SCRDIR=/home/xzhfood/gaussian/g09/scratch
source$g09root/g09/bsd/g09.profile
#gaussian-view
exportGV_DIR=/home/xzhfood/gaussian/gv
exportLIBPATH=/home/xzhfood/gaussian/gv/lib
exportLD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/xzhfood/gaussian/gv/lib
exportPATH=$PATH:/home/xzhfood/gaussian/gv
alias gv='gview.exe'
source/home/xzhfood/.bashrc
看到网上有篇QM/MM计算的教程，成功运行，计算结果正确。
[xzhfood@bogon gaussian-amber]$ ll
total 1016
-rw-rw-r--. 1 xzhfood xzhfood 259 Dec 16 22:54 amber-g09-min.in
-rw-rw-r--. 1 xzhfood xzhfood 11432 Dec 22 09:03 amber-g09-min.out
-rw-rw-r--. 1 xzhfood xzhfood 1070 Dec 22 09:03 amber-g09-min.rst
-rw-rw-r--. 1 xzhfood xzhfood 1 Dec 22 09:03 fort.351
-rw-r--r--. 1 root root 880640 Dec 22 09:03 gau_job.chk
-rw-rw-r--. 1 xzhfood xzhfood 1070 Dec 16 22:50 his.crd
-rw-rw-r--. 1 xzhfood xzhfood 1951 Dec 16 22:50 his-ini.pdb
-rw-rw-r--. 1 xzhfood xzhfood 25840 Dec 16 22:50 his.top
-rw-rw-r--. 1 xzhfood xzhfood 9174 Dec 16 22:50 leap.log
-rw-rw-r--. 1 xzhfood xzhfood 412 Dec 22 09:03 mdinfo
-rw-r--r--. 1 root root 3663 Dec 22 09:03 old.gau_job.inp
-rw-r--r--. 1 root root 48302 Dec 22 09:03 old.gau_job.log
>>> Running calculations with Gaussian <<<
| &gau
| method = BLYP
| basis = 6-31G
| scf_conv = 8
| charge = 0
| spinmult = 1
| ntpr = 50
| num_threads = 1
| verbosity = 0
| dipole = F
| use_templte = F
| /
| Program g09 found!
| Executable location: /home/xzhfood/gaussian/g09/g09
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.6571E+05 1.2411E+03 7.1568E+03 H 25
BOND = 0.0206 ANGLE = 0.4312 DIHED = 16.9792
VDWAALS = 792.1448 EEL = -82.0092 HBOND = 0.0000
1-4 VDW = 5.5589 1-4 EEL = 44.7113 RESTRAINT = 0.0000
EXTERNESCF = -166492.6739
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
10 -1.6643E+05 5.4789E+01 2.3801E+02 N 24
BOND = 3.8217 ANGLE = 1.4172 DIHED = 17.0026
VDWAALS = 79.5706 EEL = -82.0674 HBOND = 0.0000
1-4 VDW = 5.2731 1-4 EEL = 44.3566 RESTRAINT = 0.0000
EXTERNESCF = -166495.5806
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| QMMM 81.93 (100.0% of Force)
| Force time 81.93 (100.0% of Runmd)
| Runmd Time 81.93 (99.71% of Total)
| Other 0.24 ( 0.29% of Total)
| Total time 82.17 (100.0% of ALL )
| Highest rstack allocated: 110
| Highest istack allocated: 22
| Final Performance Info:
| -----------------------------------------------------
| Average timings for all steps:
| Elapsed(s) = 81.93 Per Step(ms) = 81934.43
| ps/day = 1.055 seconds/ns = 81934.43
| -----------------------------------------------------
| Job began at 09:02:34.142 on 12/22/2019
| Setup done at 09:02:34.383 on 12/22/2019
| Run done at 09:03:56.317 on 12/22/2019
| wallclock() was called 387 times
但是采用同样的方法，在台式电脑上安装配置了gaussian E01和Amber12，发现sander调用不了gaussian09,不知道问题出在哪里？
特请教各位前辈，非常感谢！
[xzhfood@localhost gam-amber]$ sander -O -i amber-g09-min.in -o amber-g09-min.out -c his.crd -p his.top -r amber-g09-min.rs
很快就结束了，g09没有启动，出现了下面文件：
[xzhfood@localhost gam-amber]$ ll
total 396
-rw-rw-r--. 1 xzhfood xzhfood 259 Dec 21 11:08 amber-g09-min.in
-rw-rw-r--. 1 xzhfood xzhfood 9424 Dec 21 21:39 amber-g09-min.out
-rw-rw-r--. 1 xzhfood xzhfood 1070 Dec 21 11:07 his.crd
-rw-rw-r--. 1 xzhfood xzhfood 1951 Dec 21 11:07 his-ini.pdb
-rw-rw-r--. 1 xzhfood xzhfood 25840 Dec 21 11:07 his.top
-rw-rw-r--. 1 xzhfood xzhfood 14076 Dec 21 11:07 leap.log
-rw-rw-r--. 1 xzhfood xzhfood 0 Dec 21 11:09 mdinfo
-rw-rw-r--. 1 xzhfood xzhfood 81 Dec 21 21:05 mdout
-rw-rw-r--. 1 xzhfood xzhfood 524288 Dec 21 21:30 y.chk
-rw-rw-r--. 1 xzhfood xzhfood 19 Dec 21 21:30 y.fchk
..................................
3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------
| Please also cite the following work for the use of the QM/MM interface:
| A. W. G"otz, M. A. Clark, R. C. Walker
| "An extensible interface for ab initio QM/MM molecular dynamics simulations
| with AMBER"
| J. Comput. Chem. 2013
| DOI: 10.1002/jcc.23444
Constants for unit conversion taken from
Mohr, Taylor, Newell, Rev. Mod. Phys. 80 (2008) 633-730
and using the thermochemical calorie (1 cal = 4.184 J):
A_TO_BOHRS = 1.889726132873E+00
AU_TO_KCAL = 6.2750946943E+02
AU_TO_DEBYE = 2.54174623E+00
>>> Running calculations with Gaussian <<<
后面没有了，g09没有启动，不知道为什么？
作者Author: sobereva 时间: 2019-12-22 15:57
先确保当前机子里直接用g09命令能启动Gaussian
作者Author: hhhnano 时间: 2019-12-22 17:38
本帖最后由 hhhnano 于 2019-12-22 17:48 编辑
当前centos 系统可以启动g90:
[xzhfood@bogon ~]$ g09
Entering Gaussian System, Link 0=g09
现在运行又多了两行：
>>> Running calculations with Gaussian <<<
SANDER BOMB in subroutine get_namelist (qm2_extern_gau_module)
The charge and spin keywords are deprecated
Please specify charge (qmcharge) and spin multiplicity (spin) in the &qmmm namelist.
可是教程里面没有spin参数设置。
作者Author: sobereva 时间: 2019-12-22 19:43
提示都写了在&qmmm字段指定电荷和自旋，补上就完了
有问题首先想着看手册啊
很多教程要么不靠谱，要么跟当前版本的情况不对应
作者Author: hhhnano 时间: 2020-1-15 00:18
谢谢SOB老师指导。
作者Author: tanshy 时间: 2022-2-23 21:24
请问sob老师和楼主~我也出现同样的问题，但是我的in文件里&qmmm有指定qmcharge和spin。该怎么解决呢？用的是amber20的sander，in文件如下：
Example QM/MM input for Sander - Gaussian interface
&cntrl
imin=1, maxcyc=10,
ntb=0,
cut=20.,
ifqnt=1
&end
&qmmm
qmmask='@11-21'
qmcharge=0,
spin=1,
qm_theory='EXTERN',
qmcut=20.0
&end
&gau
method = 'BLYP',
basis = '6-31G**',
charge = 0
&end
out文件末尾：
3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------
| Please also cite the following work for the use of the QM/MM interface:
| A. W. G"otz, M. A. Clark, R. C. Walker
| "An extensible interface for ab initio QM/MM molecular dynamics simulations
| with AMBER"
| J. Comput. Chem. 35 (2014) 95-108.
| DOI: 10.1002/jcc.23444
Constants for unit conversion taken from
Mohr, Taylor, Newell, Rev. Mod. Phys. 80 (2008) 633-730
and using the thermochemical calorie (1 cal = 4.184 J):
A_TO_BOHRS = 1.889726132873E+00
AU_TO_KCAL = 6.2750946943E+02
AU_TO_DEBYE = 2.54174623E+00
>>> Running calculations with Gaussian <<<
SANDER BOMB in subroutine get_namelist (qm2_extern_gau_module)
The charge and spin keywords are deprecated
Please specify charge (qmcharge) and spin multiplicity (spin) in the &qmmm namelist.
命令如下：
sander -O -i amber-g09-min.in -o amber-g09-min.out -c his.crd -p his.top -r amber-g09-min.rst
作者Author: Maeterlinck 时间: 2023-11-3 16:11
您好，您的问题解决了嘛， 我也遇到了相同问题
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