[gmx-users] protein membrane system

[Justin Lemkul]

On 12/25/12 2:42 AM, Shima Arasteh wrote:
>
>
>
> Hi all,
>
> I'm trying to simulate a system of POPC- Protein- Water- Ion following the Justin's tutorial of Kalp15-DPPC.
>
> I get the system-solved-ion.gro and run energy minimization. I saw some water molecules in em.gro file, therefore, I erase them and then again save the .gro file as a new one.
> But when I make a new index file, updated the top file and then go through the NVT simulation, I get this fatal error:
>
> Warning: atom name 33908 in topol.top and em.gro does not match (HW2 - HW1)
> Warning: atom name 33909 in topol.top and em.gro does not match (OW - HW2)
> Warning: atom name 33910 in topol.top and em.gro does not match (HW1 - OW)
> (more than 20 non-matching atom names)
>
> WARNING 1 [file topol.top, line 57]:
>    43770 non-matching atom names
>    atom names from topol.top will be used
>    atom names from em.gro will be ignored
>
>
> Setting gen_seed to 2957
> Velocities were taken from a Maxwell distribution at 310 K
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/readir.c, line: 1406
>
> Fatal error:
> 38 atoms are not part of any of the T-Coupling groups
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>

The mismatch implies that your atom mapping is off by one entry, indicating that 
either the update to your topology is wrong or that you deleted only part of 
some molecule, leaving a fractional species somewhere.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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