On 6/29/12 9:04 AM, Shima Arasteh wrote:
Hi,
Check out the order of sections which you have included in your .top file. I
always got this error because of the wrong orders of sections.
Incorrect order will lead to a series of "non-matching atom names" in the grompp
output. In this case, the error comes from incorrect usage of genion (see my
previous post).
-Justin
Cheers,
Shima
________________________________
From: "[email protected]"
<[email protected]>
To: [email protected]
Sent: Friday, June 29, 2012 5:24 PM
Subject: [gmx-users] error with grompp
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.
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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