[gmx-users] genion error!

Erik Marklund erikm at xray.bmc.uu.se
Wed Feb 28 09:26:06 CET 2007

Something seems wrong with your topology. It seems grompp gets  
confused about CL in one file being Na in the other. Maybe you added  
the last lines to cln.top in the wrong order. It doesn't necessarily  
cause the LINCS error later on, but suggests that your topology may  
need some more work.


28 feb 2007 kl. 09.23 skrev Qiang Zhong:

> Dear users:
>      I want to prepare protein simulation on 0.15mol/l salt  
> concentration,I use
> genion command to add ions,After genion,I change cln.top file last  
> line to NA+
> 61,CL- 41.
>    When I execute grompp ,there are warning :
> Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na)
> ........
> (more than 20 non-matching atom names)
> WARNING 1 [file "cln.top", line 9059]:
>   102 non-matching atom names
>   atom names from cln.top will be used
>   atom names from cln_b4em.gro will be ignored
> I continue to execute "mdrun nice 0 -v -s cln_em.tpr -o  
> minim_traj.trr -c
> minimized.gro -e minim_ener.edr",There are some error:
> Fatal error:
> Too many LINCS warnings (10190) - aborting to avoid logfile runaway.
> This normally happens when your system is not sufficiently  
> equilibrated,or if you
> are changing lambda too fast in free energy simulations.
> If you know what you are doing you can adjust the lincs warning  
> threshold
> in your mdp file, but normally it is better to fix the problem.
>  I don't know what happen ,could somebody tell me?
>   Thank you very much!
> pdb2gmx -f 4cln.pdb -o cln.gro -p cln.top
> editconf -f cln.gro -o cln.gro -bt octahedron -c -d 0.75
> genbox -cp cln.gro -cs spc216.gro -o cln_b4ion.gro -p cln.top
> grompp -f minim.mdp -c cln_b4ion.gro -p cln.top -o cln_b4ion.tpr
> genion -s cln_b4ion.tpr -o cln_b4em.gro -conc 0.15 -neutral
> grompp -f minim.mdp -c cln_b4em.gro -p cln.top -o cln_em.tpr
> mdrun -nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e
> minim_ener.edr
> grompp -f fullmd_sol.mdp -c minimized.gro -p cln.top -o fullmd.tpr
> mdrun -nice 0 -v -s fullmd.tpr -o md_traj.trr -x md_traj.xtc -c  
> md_final.gro -e
> md_ener.edr
> ------------------------------
> Qiang Zhong
> Key Lab of Agricultural Animal Genetics, Breeding and Reproduction  
> of Ministry of Education
> College of Animal Sciences and Technology
> Huazhong Agricultural University
> Wuhan,Hubei, 430070
> PR China
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys

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