各位,我在用amber的MM_PBSA模块做能量分解的时候,计算的时候出错,提示是这样的 Init data
    Presuming executables of amber suite to be in /home/yangbo/amber9/exe
=>> Reading input parameters
    Found PREFIX => 1A1L_ptein_DNA
    Found PATH => ../
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ../protein_NO_water_Na.top
    Found RECPT => ../protein_DNA.top
    Found LIGPT => ../protein_protein.top
    Found GC => 0
    Found AS => 0
    Found DC => 1
    Found MM => 1
    Found GB => 1
    Found PB => 0
    Found MS => 0
    Found NM => 0
    Found DCTYPE => 2
    Found COMREC => 89-110
    Found COMLIG => 1-88
    Found COMPRI => 1-88 89-110
    Found RECRES => 1-22
    Found RECPRI => 1-22
    Found RECMAP => 89-110
    Found LIGRES => 1-88
    Found LIGPRI => 1-88
    Found LIGMAP => 1-88
    Found DIELC => 1.0
    Found IGB => 2
    Found GBSA => 2
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found INTDIEL => 1.0
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00
=>> Checking sanity
    Checking GENERAL
    Implicit SAS calc by sander
    Checking DC
    Checking MM
    Checking GB
=>> Creating input
    Sander input
=>> Calculating energy / entropy contributions
    Calc contrib for ../1A1L_ptein_DNA_com.crd.1
        Calc MM/GB/SAS
bad atom type: ZN
        /home/yangbo/amber9/exe/sander -O -i sander_com.in -o sander_com.1.out -c ../1A1L_ptein_DNA_com.crd.1 -p ../protein_NO_water_Na.top not successful

现在可以判断是程序不认识ZN,但是也没有其他的提示,不知道要从哪里修改才好.请有经验的同行提出宝贵意见.谢谢

Is atom type 'ZN' defined in protein_NO_water_Na.top?

如果之前跑轨迹的时候也没有提示出错，top文件本身没什么问题。
设GB=0试试是否还有提示。

see:
http://amber.ch.ic.ac.uk/archive/200305/0160.html
可能得改源程序

跑动力学的时候完全没有问题,top文件中也是有ZN的参数.现在也在怀疑是不是要修改源程序,但是这个工作具体如何做还是个问题,而且也不清楚它到底想要锌的什么参数.还请多关注谢谢呀~~

如果GB=0,依然是不成功,不过好象错误转移了
[node4@wang 05_MMPBSA_Decomp_Residue]$ mm_pbsa.pl mm_pbsa.in

=>> Init data
    Presuming executables of amber suite to be in /opt/amber9/exe

=>> Reading input parameters
    Found PREFIX => 1A1L_ptein_DNA
    Found PATH => ../
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ../protein_NO_water_Na.top
    Found RECPT => ../protein_DNA.top
    Found LIGPT => ../protein_protein.top
    Found GC => 0
    Found AS => 0
    Found DC => 1
    Found MM => 1
    Found GB => 0
    Found PB => 0
    Found MS => 0
    Found NM => 0
    Found DCTYPE => 2
    Found COMREC => 89-110
    Found COMLIG => 1-88
    Found COMPRI => 1-88 89-110
    Found RECRES => 1-22
    Found RECPRI => 1-22
    Found RECMAP => 89-110
    Found LIGRES => 1-88
    Found LIGPRI => 1-88
    Found LIGMAP => 1-88
    Found DIELC => 1.0
    Found IGB => 2
    Found GBSA => 2
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found INTDIEL => 1.0
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00

=>> Checking sanity
    Checking GENERAL
    Checking DC
    Checking MM

=>> Creating input
    Sander input

=>> Calculating energy / entropy contributions
    Calc contrib for ../1A1L_ptein_DNA_com.crd.1
        Calc MM/GB/SAS
        /opt/amber9/exe/sander -O -i sander_com.in -o sander_com.1.out -c ../1A1L_ptein_DNA_com.crd.1 -p ../protein_NO_water_Na.top not successful
同时在输出文件 sander_com.1.out里出现这样的提示
   2.  CONTROL  DATA  FOR  THE  RUN
--------------------------------------------------------------------------------



General flags:
     imin    =       1, nmropt  =       0

Nature and format of input:
     ntx     =       1, irest   =       0, ntrx    =       1

Nature and format of output:
     ntxo    =       1, ntpr    =      50, ntrx    =       1, ntwr    =     500
     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =       0
     ioutfm  =       0, ntwprt  =       0, idecomp =       2, rbornstat=      0

Potential function:
     ntf     =       1, ntb     =       0, igb     =       0, nsnb    =   99999
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     = 999.00000, intdiel =   1.00000
     scnb    =   2.00000, scee    =   1.20000

Frozen or restrained atoms:
     ibelly  =       0, ntr     =       0

Energy minimization:
     maxcyc  =       1, ncyc    =       0, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010

IDECOMP is not compatible with EWALD

*** input error(s)

你设GB=1，MS=1看看。

缺的是计算SASA的原子参数，Zn在LCPO方法的原文献中没有定义，所以得添到源程序里

谢谢! 恩应该是您说的那种情况,我根据提示在amber9/src/sander/mdread.f目录下找到了相关的源程序.在1222-1233行可以找到相关的添加锌的原子参数的地方.但是问题是不知道应该添加什么东西?如果是锌的原子参数的话,我们手头上也没有这些数据呀.我想这个可能不是个小问题...谢谢指点~~不知道能否找到解决的方法

设置GB=1MS=1也是有问题的.
[node4@wang 05_MMPBSA_Decomp_Residue]$ mm_pbsa.pl mm_pbsa.in

=>> Init data
    Presuming executables of amber suite to be in /opt/amber9/exe

=>> Reading input parameters
    Found PREFIX => 1A1L_ptein_DNA
    Found PATH => ../
    Found COMPLEX => 1
    Found RECEPTOR => 1
    Found LIGAND => 1
    Found COMPT => ../protein_NO_water_Na.top
    Found RECPT => ../protein_DNA.top
    Found LIGPT => ../protein_protein.top
    Found GC => 0
    Found AS => 0
    Found DC => 0
    Found MM => 0
    Found GB => 1
    Found PB => 0
    Found MS => 1
    Found NM => 0
    Found DCTYPE => 2
    Found COMREC => 89-110
    Found COMLIG => 1-88
    Found COMPRI => 1-88 89-110
    Found RECRES => 1-22
    Found RECPRI => 1-22
    Found RECMAP => 89-110
    Found LIGRES => 1-88
    Found LIGPRI => 1-88
    Found LIGMAP => 1-88
    Found DIELC => 1.0
    Found IGB => 2
    Found GBSA => 2
    Found SALTCON => 0.00
    Found EXTDIEL => 80.0
    Found INTDIEL => 1.0
    Found SURFTEN => 0.0072
    Found SURFOFF => 0.00

=>> Checking sanity
    Checking GENERAL
    Checking GB
    Checking MS
Param PROBE does not exist

没设PROBE选项导致的。开了大选项需要要把下面的小选项设上。就设PROBE=0.0看看。

如果不行，那就直接源程序加LCPO的参数好了。
Zn在体系中应该数量很少，参数有些偏差对结果没有大碍，LCPO方法本身就有偏差。
Zn2+和Mg2+半径差不多，vdw半径、Probe(1.4A)、P1~P4的参数就用程序里面已经有的Mg的就行。如果体系里没有Mg，直接改个名成Zn应该就行。
实际上就是LCPO原文里的sp3、2 bonded-neighbor的氧的SASA参数，见Appendix.B

非常感谢sobereva给予的指导,您所说的这两种可能解决问题的方法,我还在进一步尝试当中.等结果出来,有什么问题还希望能与您进行深入的讨论.不过您对知识的掌握程度真是很令人佩服.祝福好运!

经过尝试我在amber9/src/sander/mdread.f目录下的相关的源程序的1222-1233行可以找到类似的Mg的参数,然后根据mg的参数完全设置成ZN的(把名字换成ZN的其他的参数均是用的Mg的),结果执行计算仍然说找不到ZN的原子类型,这回可真是很奇怪了.

mdread.f除了src\sander下面，在src\pbsa下面还有一个mdread.f，把这个也改一下。搜索全部源程序文件，能导致提示"bad atom type"的就这两个文件，如果两个都改了还是提示出错，那应该还是没改对。

我把第二处也改了,不过还是有同样的提示错误.我看他的提示中是说/amber9/exe下面的sander出了问题,我想去找这个sander发现改不了,都是绿色显示的,提示说not a directory
=>> Creating input
    Sander input

=>> Calculating energy / entropy contributions
    Calc contrib for ../1A1L_ptein_DNA_com.crd.1
        Calc MM/GB/SAS
bad atom type: ZN
        /home/yangbo/amber9/exe/sander -O -i sander_com.in -o sander_com.1.out -c ../1A1L_ptein_DNA_com.crd.1 -p ../protein_NO_water_Na.top not successful

改过源程序后重新编译amber了么？
看看/exe下可执行文件的创建时间，确保是新编译出来的

[ 本帖最后由 sobereva 于 2008-5-11 03:32 编辑 ]

没有编译过,我对程序这方面是一点都不懂.只是把程序里的数据改了一下,是不是得重新编译过才能使用呀.不知道sobereva能否帮忙.太感谢了