[gmx-users] Problems with g_membed tools

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 10 14:28:37 CET 2011

On 11/11/2011 12:05 AM, LindaSong wrote:
>  Hello all,
> I want to use g_membed to insert a protein in POPC. I followed the 
> manual steps. I used the grompp to generate the tpr file. It works 
> well. But when I handed this tpr file to g_membed, it returned this:
> -------------------------------------------------------
> Program g_membed, VERSION 4.5.3
> Source code file: gmx_membed.c, line: 688
> Fatal error:
> Trying to remove more lipid molecules than there are in the membrane
> -------------------------------------------------------
> Why it tries to remove more lipid molecules than there are in the 
> membrane?
> The membrane has 256 lipid molecules. I used PyMol to see the 
> structure of the protein with POPC. The lipids cover the whole protein.
> I don't know what's wrong here.

We can't know, because you haven't given us information like command 
lines and output copied from your terminal so we can see the diagnostic 
information g_membed printed for you.

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