[gmx-users] ions problem

[ahmet yıldırım]

Dear Justin,

Thank you. Problem is solved.  I forgot remove ions from SOL numbers.
By the way, I used the genion command as "genion -s em.tpr -o solvated.gro
-pname NA+ -np 15 -g em.log" but it correctly worked.

Thanks



16 Nisan 2011 21:37 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> I am using gromacs 4.5.3. Initially I removed ligands from pdb file. Then
>> I started to simulation .I met such a problem ( last error) after I added
>> ions. What could be the problem?
>> pdb2gmx -f withoutligand_xxx.pdb
>> editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
>> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
>> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>>
>> *Fatal Error:*
>> System has non-zero total charge: -1.500000e+01
>>
>> genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log
>>
>
> Unless you updated your topology manually after running this command, you
> haven't accounted for the fact that 15 water molecules are going to be
> removed.  Use the -p flag to have genion make the changes for you.  Note
> that "NA+" is incorrect for version 4.5.3 - ion [moleculetype] names have
> changed since version 4.0.7.
>
>
>  select: Group 13 (SOL)
>> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>> *Fatal error:*
>> number of coordinates in coordinate file (solvated.gro, 106473)
>> does not match topology (topol.top, 106518)
>>
>>
> The answer to this error is _always_ the same - you haven't accounted
> properly for some change in the system that has been made to the coordinate
> file but not the topology.
>
>
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>
>  _*topol.top:*_
>>
>> ..
>> [ molecules ]
>> ; Compound        #mols
>> Protein_chain_A     1
>> Protein_chain_B     1
>> SOL                   185
>> SOL                   143
>> SOL                33723
>> NA                       15
>>
>>
> Something isn't matching up here.  Either your genion command that you
> showed above is wrong, or this topology snippet has been modified from what
> genion would produce.  Please always copy and paste commands, topology
> snippets, etc so that we have self-consistent information to help you.
>
> -Justin
>
>  --
>> Ahmet YILDIRIM
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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-- 
Ahmet YILDIRIM
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