On 6/29/12 9:20 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
thank you for your answer.
So you mean that I should only name NA and CL like this:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA -nname CL
This is a correct command.
But when I now want to run the alraedy mentioned grompp command I get the
error:
No such moleculetype NA
What does your [molecules] directive specify? Have you cleaned up the topology
from the prior (incorrect) invocation of genion/grompp?
Can this be because of the wrong including order? I included everything
this order:
The order of #include statements is irrelevant. The only order that matters is
in [molecules], which must match the contents of the coordinate file.
-Justin
; Include forcefield parameters
#include "amber03.ff/forcefield.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "amber03.ff/tip3p.itp"
; Include topology for ions
#include "amber03.ff/ions.itp"
#include "amber03.ff/spc.itp"
#include "amber03.ff/dum.itp"
Bests Eva
On 6/29/12 8:54 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I added ions to the solvent around my structure with the command:
genion -s 3m71_minim.tpr -o 3m71_minim_ion.gro -p 3m71.top -conc 0.1
-neutral -pname NA+ -nname CL-
and then I select the 13 (SOL)
Now I have in my topology file
[ molecules ]
; Compound #mols
Protein_chain_A 1
DUM 30066
SOL 14305
NA+ 32
CL- 32
which is correct in my opinion.
Well, it is a correct outcome of genion, but it is incorrect usage. From
genion -h:
"The ion molecule type, residue and atom names in all force fields are the
capitalized element names without sign. This molecule name should be given
with -pname or -nname, and the [molecules] section of your topology
updated
accordingly, either by hand or with -p. Do not use an atom name instead!"
-Justin
But now when I want to run grompp:
grompp -v -f minim_solv.mdp -c 3m71_minim_ion.gro -p 3m71.top -o
3m71_minim_ion.tpr 2>>logErr 1>>logOut
I always get the error:
No such moleculetype NA+
although I already included the ion topology file:
; Include topology for ions
#include "amber03.ff/ions.itp"
What is wrong here?
Best Eva
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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