[gmx-users] genion error!

Yang Ye leafyoung81-group at yahoo.com
Wed Feb 28 13:19:02 CET 2007

On 2/28/2007 7:52 PM, Mark Abraham wrote:
> Qiang Zhong wrote:
>> 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:
> Hardly surprising... most gromacs warnings should be considered 
> carefully.
I think what Mark means is that in such case, you shall not continue to 
run mdrun without inspecting the warnings.
> First the atom names in your .gro and .top files have to match those 
> in the .atp files for the force field you're using. Then check the 
> order and number of Na and Cl are correct.
> Mark
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