PreProcessorError: Bad #include syntax

[marioernestovaldes]

I have run a simulation for a protein-ligand complex using amber99 force field（amber 99 for protein，acpype for ligand） in GROMACS and when I tried to run gmx_MMPBSA it gave me this error

[INFO ] Building Normal Complex Amber topology... File "/home/lixin347/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa app.make_prmtops() File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 689, in make_prmtops self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology() File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 125, in buildTopology tops = self.gmxtop2prmtop() File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 534, in gmxtop2prmtop com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM']) File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 821, in cleantop rtemp_top = parmed.gromacs.GromacsTopologyFile(ttp_file.as_posix()) File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 251, in init self.read(fname, defines, parametrize) File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/gromacstop.py", line 289, in read for line in f: File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_gromacsfile.py", line 44, in iter for line in self._handle: File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 175, in iter self._ppcmdmap[cmd](self, args) File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 30, in wrapper return func(self, args) File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/gromacs/_cpp.py", line 279, in _pp_include raise PreProcessorError('Bad #include syntax') PreProcessorError: Bad #include syntax Exiting. All files have been retained.

_Originally posted by @347lixin in https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/84#issuecomment-1477752985_

[marioernestovaldes]

This seems to be something related to the topology format... could you please attach the topology file?

[347lixin]

This is my data of MD 100 ns,topol.top is in it, protein CD36 is generated by amber99 force field, ligand daidzein (DAI) is generated by acpype.

------------------ 原始邮件 ------------------ 发件人: "Valdes-Tresanco-MS/gmx_MMPBSA" @.>; 发送时间: 2023年3月22日(星期三) 凌晨1:22 @.>; @.**@.>; 主题: Re: [Valdes-Tresanco-MS/gmx_MMPBSA] PreProcessorError: Bad #include syntax (Issue #359)

This seems to be something related to the topology format... could you please attach the topology file?

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从QQ邮箱发来的超大附件

MD of CD36_daidzin 100 ns.zip (2.52G, 2023年04月21日 02:23 到期)进入下载页面：https://mail.qq.com/cgi-bin/ftnExs_download?k=37663263f9e7e36ba4e21e314562561a1d1202015b03520248040053514f5705045f1f535303051853520506510705045d040551637f647821465d0543212006533956020a061e5c0b46035353420a464b1c5b13635f&t=exs_ftn_download&code=ef2ccbd5

[Valdes-Tresanco-MS]

Commonly acpype generates topologies with format problems, for example, space before # statement, missing ;, etc. Please, make sure that the topology format is correct. Also, I don't sure if a response via email sends the files as expected. A better option is to share these files via Google Drive, One Drive, or any other platform, and give us the access permission

[347lixin]

I uploaded the file in google drive. please open this link: https://drive.google.com/file/d/1l05esa3Eli_eaG9cF2LkpFdMuk4US_qG/view?usp=sharing,thank you very much.

------------------ 原始邮件 ------------------ 发件人: "Valdes-Tresanco-MS/gmx_MMPBSA" @.>; 发送时间: 2023年3月22日(星期三) 凌晨3:06 @.>; @.**@.>; 主题: Re: [Valdes-Tresanco-MS/gmx_MMPBSA] PreProcessorError: Bad #include syntax (Issue #359)

Commonly acpype generates topologies with format problems, for example, space before # statement, missing ;, etc. Please, make sure that the topology format is correct. Also, I don't sure if a response via email sends the files as expected. A better option is to share these files via Google Drive, One Drive, or any other platform, and give us the access permission

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

[marioernestovaldes]

line 22 the quotation marks are missing... it should be

include "CD36.itp"

let me know if that solves the problem

[347lixin]

this problem is solved，but another problem is generated，when i increase this command in mmpbsa.in file： / &decomp idecomp=2, dec_verbose=3 print_res="within 4" / 

new error is generated

[INFO   ] Selecting residues by distance (4 Å) between receptor and ligand for decomposition analysis... [INFO   ] Selected 22 residues: R:A:ARG:63  R:A:ARG:96  R:A:LYS:100 R:A:PHE:114 R:A:GLN:116 R:A:ASN:118 R:A:PHE:201 R:A:TYR:202 R:A:PRO:203 R:A:TYR:204 R:A:ASP:209 R:A:TYR:212 R:A:ASP:250 R:A:PHE:267 R:A:SER:268 R:A:SER:269 R:A:ASP:270 R:A:LYS:334 R:A:ARG:337 R:A:LYS:385 R:A:GLU:418 L:B:DAI:435

[INFO   ] Cleaning normal complex trajectories... [INFO   ] Building AMBER topologies from GROMACS files... Done.

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

[INFO   ] 201 frames were processed by cpptraj for use in calculation. [INFO   ] Starting calculations in 1 CPUs...

[INFO   ] Running calculations on normal system... [INFO   ] Beginning PB calculations with /home/lixin347/miniconda3/envs/gmxMMPBSA/bin/sander [INFO   ]   calculating complex contribution...               0%|                                                                  | 0/201 [elapsed: 00:00 remaining: ?]At line 143 of file /home/conda/feedstock_root/build_artifacts/ambertools_1645002103866/work/AmberTools/src/sander/rgroup.F90 (unit = 5, file = '_GMXMMPBSA_pb_decomp_com.mdin') Fortran runtime error: End of file

Error termination. Backtrace:

0  0x7f97fad72068 in read_sf_internal

        at ../../../libgfortran/io/transfer.c:325

1  0x7f97fad6fd7d in read_default_char1

        at ../../../libgfortran/io/read.c:455

2  0x7f97fad73007 in formatted_transfer_scalar_read

        at ../../../libgfortran/io/transfer.c:1787

3  0x7f97fad73c66 in formatted_transfer

        at ../../../libgfortran/io/transfer.c:2491

4  0x55cf4b18c6b8 in ???

5  0x55cf4b1169fa in ???

6  0x55cf4b0c281f in ???

7  0x55cf4b0bffb6 in ???

8  0x55cf4b0c002e in ???

9  0x7f97faa30082 in ???

10  0x55cf4aef4098 in ???

[ERROR  ] CalcError /home/lixin347/miniconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!

If you are using sander and PB calculation, check the *.mdout files to get the sander error .            Check the gmx_MMPBSA.log file to report the problem.   File "/home/lixin347/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>     sys.exit(gmxmmpbsa())   File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa     app.run_mmpbsa()   File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa    self.calc_list.run(rank, self.stdout)   File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run    calc.run(rank, stdout=stdout, stderr=stderr)   File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 625, in run    GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) +   File "/home/lixin347/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in init     raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.') CalcError: /home/lixin347/miniconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!

If you are using sander and PB calculation, check the *.mdout files to get the sander error

Check the gmx_MMPBSA.log file to report the problem. Exiting. All files have been retained.

------------------ 原始邮件 ------------------ 发件人: "Valdes-Tresanco-MS/gmx_MMPBSA" @.>; 发送时间: 2023年3月22日(星期三) 中午12:04 @.>; @.**@.>; 主题: Re: [Valdes-Tresanco-MS/gmx_MMPBSA] PreProcessorError: Bad #include syntax (Issue #359)

line 22 the quotation marks are missing... it should be

include "CD36.itp"

let me know if that solves the problem

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[Valdes-Tresanco-MS]

This is a known bug in v1.6.0 that we already fixed (#346, #352). We are compiling other reported problems to release v1.6.1. Please, install the development version until we release the next one.

python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.git -U

[347lixin]

thank you very much

---Original--- From: "Mario Sergio Valdés @.> Date: Wed, Mar 22, 2023 23:50 PM To: @.>; Cc: @.**@.>; Subject: Re: [Valdes-Tresanco-MS/gmx_MMPBSA] PreProcessorError: Bad #includesyntax (Issue #359)

This is a known bug in v1.6.0 that we already fixed (#346, #352). We are compiling other reported problems to release v1.6.1. Please, install the development version until we release the next one. python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.git -U

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[347lixin]

Dear professor, I caculated MMPBSA in WSL(Windows subsystem for linux) by gmx_MMPBSA, but this subsystem in not launched gmx_MMPBSA_ana, is there any method to install gmx_MMPBSA_ana in windows system,thank you very much.

------------------ 原始邮件 ------------------ 发件人: "Valdes-Tresanco-MS/gmx_MMPBSA" @.>; 发送时间: 2023年3月22日(星期三) 晚上11:50 @.>; @.**@.>; 主题: Re: [Valdes-Tresanco-MS/gmx_MMPBSA] PreProcessorError: Bad #include syntax (Issue #359)

This is a known bug in v1.6.0 that we already fixed (#346, #352). We are compiling other reported problems to release v1.6.1. Please, install the development version until we release the next one. python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.git -U

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

[Valdes-Tresanco-MS]

There is this tutorial for able to run GUI applications in WSL I don't test it, so I don't know if working. Currently, we are working on a new version as an independent application called xBFreE-Analyzer which will run on Windows OS as well Stay tuned

[347lixin]

thank you，I try this test.

---Original--- From: "Mario Sergio Valdés @.> Date: Thu, Mar 23, 2023 13:04 PM To: @.>; Cc: @.**@.>; Subject: Re: [Valdes-Tresanco-MS/gmx_MMPBSA] PreProcessorError: Bad #includesyntax (Issue #359)

There is this tutorial for able to run GUI applications in WSL I don't test it, so I don't know if working. Currently, we are working on a new version as an independent application called xBFreE-Analyzer which will run on Windows OS as well Stay tuned

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[347lixin]

Dear Professor, I would like to ask, what type of file can the  amino acid residue with 4 A contribution energy be stored, and can it be analyzed by separately opening gmx_MMPBSA_ana later? ------------------ 原始邮件 ------------------ 发件人: "Valdes-Tresanco-MS/gmx_MMPBSA" @.>; 发送时间: 2023年3月23日(星期四) 中午1:04 @.>; @.**@.>; 主题: Re: [Valdes-Tresanco-MS/gmx_MMPBSA] PreProcessorError: Bad #include syntax (Issue #359)

There is this tutorial for able to run GUI applications in WSL I don't test it, so I don't know if working. Currently, we are working on a new version as an independent application called xBFreE-Analyzer which will run on Windows OS as well Stay tuned

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[Valdes-Tresanco-MS]

There are several ways to store information related to energy decomposition. For example, the file FINAL_DECOMP_MMPBSA.dat (-do flag) stores only the summary in flat or csv format, and the -deo flag stores all the data in csv format. You can use excel or another similar tool to process these files, use our API with other python tools or gmx_MMPBSA_ana. Our recommendation is to use our tool gmx_MMPBSA_ana for the analysis since it comprises all the resources for the analysis of these results. Please, check these discussions:

• 296

• 347

I closing this issue since the initial problem was solved. For other questions or doubts, please, feel free to open a new one