[gmx-users] Re: gmx-users Digest, Vol 74, Issue 189

[Nayef Daher]

Hi Justin

I manually modified the fws.top by removing two SOL and adding 2 CL-  
and that still didn't work.

Adding -p flag gave me another type of error, stating that  
input/output is wrong. I entered the genion command as such

genion –s fws_em.tpr –o fws_ion.gro -p fws.top –nname CL- –nn 2 –g fws_ion.log
>
> Nayef Daher wrote:
>> Hi
>>
>> I am trying to follow the tutorial listed on
>> http://eugen.leitl.org/chem/kerrigje/pdf_files/fwspidr_tutor.pdf with
>> the latest version of Gromacs, 4.0.7
>>
>> The commands I typed were
>>
>> pdb2gmx –ignh –ff G43a1 –f 1OMB.pdb –o fws.gro –p fws.top
>> editconf –f fws.gro –d 0.7
>> editconf –f out.gro –o fws_ctr.gro –center x/2 y/2 z/2
>> genbox –cp fws_ctr.gro –cs spc216.gro –o fws_b4em.gro –p fws.top
>> grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr
>> genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log
>> [select Group 12: SOL]
>> pico fws.top [reduce number of SOL by two and add 2 CL- at the end of
>> the file]
>> mdrun –s fws_em.tpr –o fws_em.trr –c fws_b4pr.gro –g em.log –e em.edr &
>> open new terminal
>> grompp –f pr.mdp –c fws_b4pr.gro –r fws_b4pr.gro –p fws.top –o fws_pr.tpr
>>
>> The error I kept getting was
>>
>> Fatal error:
>> Number of coordinates in coordinate file (fws_b4pr.gro, 4996) does not
>> match topology (fws.top 4992)
>>
>> So what additional step do I need to take (or file to re-write) in order
>> to solve this problem?
>>
>
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>
> Add the -p flag to your genion command, or update the topology manually.
>
> -Justin
>
>> Thanks!
>>
>> Nayef Daher
>> PhD Chemical Engineering
>> University of Alberta, Canada
>>
>
> --
> ========================================
>
> 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
>
> ========================================
>
>