leila karami skrev:
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:
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.
Not sure if it's related, but your topology doesn't match the gro-file.
0 Cl in top, but 1 in gro.
/Erik
--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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