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

[Justin A. Lemkul]

Nayef Daher wrote:
> 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
> 

The actual error message is the only useful information.  I suspect, however, 
that Tsjerk identified your problem.  You're going straight from genion to 
mdrun, which certainly isn't correct.  Read the tutorial more carefully, surely 
you've skipped a step.

There is no need to both use -p with genion and make manual modifications. 
Using genion -p just saves you the trouble of potentially making mistakes, which 
is what I had assumed happened.

-Justin

> 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
>>
>> ========================================
>>
>>

-- 
========================================

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

========================================