John Bennett wrote:
Dear Gromacs Users,
I created a starting structure that includes 100 n-dodecane molecules (
pdb file ) using packmol. And I want to use the packmol pdb file in
Gromacs 3.3 . Can I directly start generating Gromacs top and crd file
with using pdb2gmx ? For example to use a packmol pdb file in Amber it
As long as you have a suitable topology, you do not need to use pdb2gmx (which
probably doesn't have an entry for n-dodecane in any of the force fields, anyway).
is necessary to add TER cards betwen each seperate molecule. Are there
anything like that I must do for using packmol pdb file in Gromacs ? And
units in packmol pdb file is angstrom . So Should I convert units to nm
Gromacs can use .pdb files as input.
? Finally What is the latest stable version of Gromacs ? I think Gromacs
4.0.3 is still a beta version ?
Version 4.0.4 is the latest stable version (4.0.3 was not a beta, either).
-Justin
Thanks in advance!
Regards
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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