[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

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


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