Error in membrane example

[LyMai10]

Dear Andrew Jewett,

I tried to run the example Coarse-grained lipid bilayer using the MARTINI force field and PACKMOL. When I run " moltemplate.sh -xyz system.xyz system.lt" comment there was an error like this.

Error: Number of atoms in coordinate file provided by user (9600) does not match the number of atoms generated in ttree file (9216)

Could you please show me how to fix this error. Ps: I didn't change any thing in your input files

Thank you in advance for your help.

Best regards

[jewettaij]

Hi LyMai10

I noticed your earlier post about the DPPC_bilayer_formation_PACKMOL example, but I couldn't get to a computer where I could install and test moltemplate yesterday. When I got home today I noticed you had erased your post. Did you resolve you issue? If so, feel free to click on the "Close" button at the bottom of this page.

More advice:

• The martini lipids examples are not as well tested as the all-atom examples. I have corrected some mistakes, but there may be more. So use caution.

• I also wanted to warn you that these MARTINI examples in moltemplate are for MARTINI version 2. However a new version of MARTINI was released a year or two ago (version 3). Moltemplate does not yet support version 3 because the ITP files from the https://cgmartini.nl website have not been converted into moltemplate (LT) format yet. (The version 2 files were converted by hand I have been hoping to write a general GROMOS ITP file converter for a while, which could convert any ITP file into moltemplate format, not just the MARTINI files. I don't have time to do this, but if you want to use MARTINI 3, and you have time to write this converter, let me know. I don't think it's a hard task, but I could be wrong. Either way, I wanted to warn you.)

  I don't check github or email more than about once per week, but if you do post a response, I will eventually reply. (Again, don't forget to click that "Close" button below, if this issue is resolved.)

[LyMai10]

Hello Andrew Jewett, Thank you so much for your kind concern. I have resolved my problem. The thing here is I took the system.xyz file obtained from GROMACS to run in the Moltemplate that cause the above error ( moltemplate.sh -xyz system.xyz system.lt). Then I just run only the file created by Moltemplate, it works well. I think that we don't need to use GROMACS any more. Related to the MARTINI version, actually we would like to try the MARTINI 3 but it need time to consider.