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标题: windows编译gmx计算mmpbsa PB项特别正，SA为0 [打印本页]

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Author: lucies123 时间: 2023-8-10 12:33
标题: windows编译gmx计算mmpbsa PB项特别正，SA为0
因为服务器出了问题，故安装了sob老师编译的windows版本的gmx2020，另安装了apbs，想要使用gmx_mmpbsa.bsh脚本计算mmpbsa，
为了在windows上使用该bash脚本，安装了git bash，在git bash下运行（./gmx_mmpbsa.sh）

但是对同一个体系重复计算（轨迹是原来在服务器上gmx2018生成的），发现PB项特别大，SA项为0，并出现了如下报错，请教下大家原因。是否和我使用git bash有关？或者相关软件编译不正确导致的调用错误？或者在windows下使用该bash脚本运行环境参数设置错误？
原来在服务器下运算结果都是正常的。

>> Warning:
!!! 1. make sure gmx is available and version is consistent
!!! 2. gawk version > 3; macOS awk version > 2018
!!! 3. watch _pid.pdb to make sure PBC is correct
--------------------------------------------------------------------------------
>> Log:
TODO:    parallel APBS, focus
2022-07-14: fix issues with Chinease in PBSAset
2022-07-08: fix bug, No PB SA value
2022-07-01: fix bug for awk too many open files
2022-06-18: fix bug for ndx when Lig is 1st
2022-04-19: fix bug for CAS
            remove -com option
2022-02-09: CAS except GLY, PRO, CYX
            fix radius bug, use AMBER mBondi
            change to AMBER PB4
2021-11-25: keep original PDB residue name
            output avaraged contibutions
            clean output files
2021-05-17: add systime and fflush, only for gawk
2021-05-16: revise cmd for all Linux
            see https://github.com/Jerkwin/gmxtool/issues/2
2021-03-14: add -cou, -ts option, see 10.1088/0256-307X/38/1/018701
            change default PB method to npbe
2021-03-03: fix bug: awk will exit for multiple system call
2020-11-15: fix bug for resID >=1000, for awk 3.x gsub /\s/
2020-06-02: fix bug of withLig
2020-06-01: fix bug of -skip
2020-05-27: fix bug for sdie
2020-05-26: fix bug for RES name
2020-04-03: use C6, C12 directly
2020-01-08: support protein only
2019-12-24: fix bug for small time step
2019-12-10: fix bug for OPLS force field
2019-11-17: fix bug for c6, c12 of old version tpr
2019-11-03: fix bug for time stamp
2019-09-19: push to gmxtool
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

>> 0. set up environmets and parameters: OK !

>> 1. preprocessing trajectory: OK !

>> 2. generate qrv file: OK !

>> 3. run MM-PBSA calculatons
>> Frame 1/3: _pid~7.5ns  MM-PBSA(with DH) = 46538.201(46572.364) kJ/mol Estimated Time Remaining: ~ 0h:01m:36s
>> Frame 2/3: _pid~7.6ns  MM-PBSA(with DH) = 46421.335(46450.069) kJ/mol Estimated Time Remaining: ~ 0h:01m:09s
                           MM-PBSA(with DH) = 46301.098(46330.617) kJ/mol Estimated Time Remaining: ~ 0h:00m:00s
awk: cmd. line:474: (FILENAME=_pid.pdb FNR=54669) warning: exp: argument 18731.6 is out of range
awk: cmd. line:474: (FILENAME=_pid.pdb FNR=54669) warning: exp: argument 18743.5 is out of range

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