[gmx-users] Re:Error:4 atoms are not part of any of the T-Couplinggroups

Qiang Zhong zqiang320 at webmail.hzau.edu.cn
Thu Feb 8 03:54:01 CET 2007

I have solved this problem by all your advices. Thank you, Mark and Yang Ye for
your help!

>That wasn't the advice Yang Ye gave you... see 
>For a simpler solution, see 

>Message: 6
>Date: Wed, 07 Feb 2007 22:29:36 +0800
>From: Yang Ye <leafyoung81-group at yahoo.com>
>Subject: Re: [gmx-users] Error:4 atoms are not part of any of the
>	T-Coupling	groups
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <45C9E250.8060407 at yahoo.com>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>Interesting that you have your Ca2+ ions in the beginning of your 
>structure file. In this case, remove the line [ SOL ] and replace [ CA ] 
>with [ SOL ].
>Although, changing your mdp file to have "Protein Non-Protein" is simpler.
>The rationale behind is that the *groups* included for the tc-grps shall 
>cover all atoms.
>On 2/7/2007 9:34 PM, Qiang Zhong wrote:
>> Hollow:
>>       I have post my question last time,my emailbox can not work, So I post
>> again.
>> I have 4 calcium ions bind at  protein, when I use command:
>>  grompp  -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o fullmd.tpr
>> I got error message:
>> Fatal error:
>> 4 atoms are not part of any of the T-Coupling groups
>> I got a advice to use :
>> make_ndx   -f  minimized_water.gro
>> Then I got a file index.ndx
>> I find the line in index.ndx ,just like below:
>> 57378 57379 57380 57381 
>> [ CA ]
>>    1    2    3    4 
>> [ SOL ]
>> Then I delete them,and run again:
>> grompp -n index.ndx -f fullmd_sol.mdp -c minimized_water.gro -p cln.top -o
>> fullmd.tpr
>> But Error still there.
>> Could somebody tell me how to do?
>> Thank you very much!

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