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molmaker.py not functioning as expected
- Jingjie Yeo
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8 years 6 months ago #5015
by Jingjie Yeo
molmaker.py not functioning as expected was created by Jingjie Yeo
I have been trying to obtain a .gro file for the pegylated lipid. i used the command
It immediately throws the error:
However, no such file exists even if I use the "-keep" flag (in fact nothing appears at all), and there are no further clues as to what is going on. Would this be related to the fact that I am using Gromacs 5.0.4?
./molmaker.py -i pegylated.itp -o test.gro -ff martini_v2.0.itpIt immediately throws the error:
grompp error: check .molmk test.pp.logHowever, no such file exists even if I use the "-keep" flag (in fact nothing appears at all), and there are no further clues as to what is going on. Would this be related to the fact that I am using Gromacs 5.0.4?
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8 years 6 months ago #5016
by mnmelo
Replied by mnmelo on topic molmaker.py not functioning as expected
Hi,
Thanks for reporting on this.
I haven't tried GROMACS 5 with molmaker yet, and my guess is that it is indeed the cause for failure (cutoff-scheme, for instance, now defaults to verlet). If you're only after the structure is it possible to just run molmaker.py with GROMACS 4?
As to the missing output, that's quite odd. You should always get that file. Note that it is a hidden file (there's a leading period in its filename); you need to run ls -a to see it.
Also, by default the prefix is '.molmk_', with an underscore, not '.molmk ' as you have in your quoted error. Did you mis-copy it here? Or was it really like that on the command-line?
Cheers and let me know,
Manel
Thanks for reporting on this.
I haven't tried GROMACS 5 with molmaker yet, and my guess is that it is indeed the cause for failure (cutoff-scheme, for instance, now defaults to verlet). If you're only after the structure is it possible to just run molmaker.py with GROMACS 4?
As to the missing output, that's quite odd. You should always get that file. Note that it is a hidden file (there's a leading period in its filename); you need to run ls -a to see it.
Also, by default the prefix is '.molmk_', with an underscore, not '.molmk ' as you have in your quoted error. Did you mis-copy it here? Or was it really like that on the command-line?
Cheers and let me know,
Manel
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8 years 6 months ago #5024
by Jingjie Yeo
Replied by Jingjie Yeo on topic molmaker.py not functioning as expected
Hi Manel,
Thank you for the information, I tested it with Gromacs 4.6 and it works fine. May I know whether it will eventually be ported to Gromacs 5.x?
Thank you for the information, I tested it with Gromacs 4.6 and it works fine. May I know whether it will eventually be ported to Gromacs 5.x?
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8 years 6 months ago #5026
by mnmelo
Replied by mnmelo on topic molmaker.py not functioning as expected
Ah, great you got it working!
Up until now there hadn't yet been a need for GROMACS 5 with it. I'll work on updating it, maybe by performing version detection.
I'll let you know here when it's done.
Cheers,
Manel
Up until now there hadn't yet been a need for GROMACS 5 with it. I'll work on updating it, maybe by performing version detection.
I'll let you know here when it's done.
Cheers,
Manel
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