leila karami wrote:
dear justin
I transfer gro files from linux to windows through SSH secure shell
program. I added 10 Na ions by genion command but in gro file following
case is appeared:
If an unrequested Cl is being added, then that is worth investigating. What was
your *exact* genion command?
Does the VMD error result in the edited file, or the one that has the additional
Cl atom?
7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991
7209Na Na23128 0.179 2.821 0.336 -0.2683 -0.1820 0.5803
7210Na Na23129 2.288 0.458 4.819 -0.1171 0.7612 -0.4903
7211Na Na23130 3.640 1.815 1.138 -0.1083 -0.1591 0.0485
7212Na Na23131 2.183 3.845 1.964 -0.0409 -0.1492 0.6725
7213Na Na23132 3.356 5.216 5.834 -0.2686 0.1059 -0.1660
7214Na Na23133 4.304 2.510 0.809 -0.2994 0.3939 0.7264
7215Na Na23134 4.609 4.931 0.535 -0.2609 0.1315 -0.1767
7216Na Na23135 5.553 6.022 5.152 0.3516 -0.2021 0.2022
7217Na Na23136 5.865 1.114 5.034 0.0442 0.0272 0.3437
*7218Cl Cl23137 0.000 0.000 0.000 0.0000 0.0000 0.0000
* 6.15463 6.21503 6.20117
I deleted line of 7218Cl Cl23137 0.000 0.000
0.000 0.0000 0.0000 0.0000
in top file following case is appeared:
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
SOL 7117
Na 10
Cl 0
I deleted last line.
I am using amber03 force field in gromacs program to study interaction
of pr-dna.
Then I know that your model is wrong. You have no N-terminal protonation
whatsoever! Think about biology before plowing ahead with computer programs
that are only capable of doing what you tell them. Under AMBER, terminal
residues require a prefix, i.e. NGLY (and CXXX for the C-terminal residues).
This has been stated many times across this list, and is clearly in the ffamber
documentation. Did you perhaps use the -missing flag with pdb2gmx when you got
an error message?
Perhaps this extra, unwanted, Cl atom is being added by genion because you have
some bizarre fractional charge on your molecule?
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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