[gmx-users] ions problem

[Justin A. Lemkul]

ahmet yıldırım wrote:
> 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.
> 

It may have "worked" but be aware that grompp will later complain about 
non-matching atom names.  In this case, it won't be a significant problem, but 
you will make your life easier if you follow the naming conventions  that are 
explained in the manual and genion help info:

"The ion molecule type, residue and atom names in all force fields are the
capitalized element names without sign. Ions which can have multiple charge
states get the multiplicity added, without sign, for the uncommon states
only."

-Justin

> Thanks
> 
> 
> 
> 16 Nisan 2011 21:37 tarihinde Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> 
> 
> -- 
> 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

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