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 <jalem...@vt.edu
<mailto:jalem...@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
========================================
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