An issue in generating topology from Gmx file

[张恒悦]

Hi,

Sorry for disturbing you! I am trying to generate topology file with the program xtp_map. After I inputted the following command, it replies

$ xtp_map -t MD_FILES/npt.tpr -c MD_FILES/PEN0.gro -s mapping.xml -f state.hdf5
==================================================
========   VOTCA (http://www.votca.org)   ========
==================================================

please submit bugs to https://github.com/votca/votca/issues

xtp_map, version 2024-dev gitid: e0a61dbe1 (compiled Feb 13 2023, 20:13:21)

an error occurred:
Error 'tpr' file format of file 'MD_FILES/npt.tpr' cannot be read or written
I am wondering why it replies as this. From the tutorials I got the knowledge and input the command as the tutorials guided me. I checked the authority of the tpr file, and it looks that there were no problems. So I am wondering how to fix this problem.

What's more, I assume that tpr file is not necessary in this command. I think that tpr file is the sum of top, gro and mdp file. And I have provided the gro file after -c flag, so I guess that only a top file is needed and what shows in mdp file is not necessary...?

I sincerely hope that you can reply when you are not busy. With my greatest gratitude!

Best regards,

Hengyue Zhang

[Victor Zh]

Hi all,

I am the one who prompted the same question yesterday. And I'd like to provide the files I tried yesterday, hoping that they could describe my problem better. It looks that everything goes well except npt.tpr. :-(

Thank you all a lot!

Hengyue Zhang

[Victor Zh]

I am the one who prompted this issue yesterday. I'd like to provide the files to describe my issue better. 

Thanks a lot, the developers!

Hengyue Zhang

[Christoph Junghans]

Quick question, is VOTCA compiled the gromacs support?

Christoph

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Christoph Junghans
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[张恒悦]

No, gromacs was compiled independently. I compiled gromacs first then votca.


---- Replied Message ----
From Christoph Junghans<jung...@votca.org> Date 02/15/2023 07:31 To vo...@googlegroups.com Cc Subject Re: [votca] Re: An issue in generating topology from Gmx file

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e7io4fNeZoPkEnF10ePU%2BPe5mcmJEUj0UDW9fzznto-dQ%40mail.gmail.com.

张恒悦 Hengyue Zhang

天津大学化工学院

地址：天津市津南区海河教育园区雅观路135号天津大学（300354）

School of Chemical Engineering and Technology, Tianjin University

Add: No. 135 Yaguan Rd., Tianjin, P. R. China (300354)

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College of Chemistry, Nankai University 

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Email: pds...@tju.edu.cn / pds...@mail.nankai.edu.cn 

Tel: +86 137 2187 2381

[Christoph Junghans]

Let me clarify: when you build votca did it pick up your gromacs install? (Check the cmake output.)

Christoph

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/AAIAmACoFuIhbYvwyQtf2arF.2.1676452666201.Hmail.3020207336%40tju.edu.cn.

[张恒悦]

Hi Christoph,

I guess that I figure out what you mean. I compiled votca again with the flag -DBUILD_OWN_GROMACS=ON, and this time this command worked well. 

Feeling sry for my poor English! Thx a lot!

Best regards,

Hengyue Zhang

发件人：Christoph Junghans <jung...@votca.org>
发送日期：2023-02-16 00:47:16
收件人：vo...@googlegroups.com
主题：Re: [votca] Re: An issue in generating topology from Gmx file

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e7DKO8FvBQpKNbaXhAedAcfKBRZP4%2B%3D7MCV0G6pkYuCpQ%40mail.gmail.com.

[Christoph Junghans]

That option will use a built-in version of gromacs and not the one you
had compiled yourself, but whatever works for you.
My guess is, you didn't build gromacs with -DGMX_INSTALL_LEGACY_API=ON
and hence VOTCA didn't pick it up.

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/ALwAHwBFFqokuXMFRGGvzarm.2.1676561546469.Hmail.3020207336%40tju.edu.cn.