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标题: 求助gmx_MMPBSA计算时没有报错不明原因停止 [打印本页]

作者
Author: 高小白123 时间: 2024-4-17 02:42
标题: 求助gmx_MMPBSA计算时没有报错不明原因停止
我在提交gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ct trj_15-20ns.xtc -ci index.ndx -cg 18 12 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat任务时一直跑不到最后，日志截止在calculating complex contribution...就停止了。
[DEBUG  ]  ->  frame 500 time 20000.000
[DEBUG  ] Last written: frame 500 time 20000.000
[DEBUG  ]
[DEBUG  ]
[DEBUG  ] GROMACS reminds you: "Nothing is more anarchic than power." (Pier Paolo Pasolini)
[DEBUG  ]
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 19: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO ] Building AMBER topologies from GROMACS files... Done.

[INFO ] Loading and checking parameter files for compatibility...
[INFO ] Preparing trajectories for simulation...

[INFO ] 501 frames were processed by cpptraj for use in calculation.
[INFO ] Running calculations [INFO ] 501 frames were processed by cpptraj for use in calculation.
[INFO ] Running calculations on normal system...
[INFO ] Beginning PB calculations with /home_gsx/soft/app/anaconda_new/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...

output的反馈是这样的
[INFO ] Beginning PB calculations with /home_gsx/soft/app/anaconda_new/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...
[INFO ] 501 frames were processed by cpptraj for use in calculation.

[INFO ] Running calculations on normal system...
[INFO ] Beginning PB calculations with /home_gsx/soft/app/anaconda_new/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...

我的in文件是在网络上找的别人的：
&general
sys_name="Prot-Lig-CHARMM",
startframe=1, #始末帧数
endframe=5000,
# In gmx_MMPBSA v1.5.0 we have added a new PB radii set named charmm_radii.
# This radii set should be used only with systems prepared with CHARMM force fields.
# Uncomment the line below to use charmm_radii set
PBRadii=5,
/
&pb
# radiopt=0 is recommended which means using radii from the prmtop file for both the PB calculation and for the NP
# calculation
istrng=0.15, fillratio=4.0, radiopt=0
/

轨迹文件进行了处理和提取
gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center -pbc mol -ur compact

gmx trjconv -f md_0_10_center.xtc -o trj_15-20ns.xtc -b 15000 -e 20000

topol文件上传了一个蛋白一个小分子和一个RNA片段的top，因为我希望蛋白和小分子整体作为受体，RNA作为配体，所以在index上定义了新组，不知道这个操作对top文件正确性有没有影响。

index文件感觉没有问题，我试了蛋白和RNA作为受体和配体输出文件也是一样的

恳请各位老师帮我看看我现在应该检查修改哪部分呢？

因为是在超算上运算，我也不知道是不是在安装ambertools的时候缺少哪个库或者路径装错了？

作者
Author: 艾小野 时间: 2024-5-23 14:54
您好，想问这个问题您解决了吗？我目前也打算跑这个，但是我是跑蛋白质和小分子物质

作者
Author: yicheng526 时间: 2025-2-10 19:34
请问解决了吗

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