Difference between revisions of "Molecular Dynamics Simulations"
From Bioinformatikpedia
(Created page with "==Preparation== * <code>repairPDB 1a6z.pdb -ssw 15t >ssw.tmp</code> but there was no crystal water included. * <code>repairPDB 1a6z.pdb -nosol >1a6z_clean.pdb</code> * <code>scwr…") |
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* <code>repairPDB 1a6z_clean_complete.pdb -noh >1a6z_final.pdb</code> |
* <code>repairPDB 1a6z_clean_complete.pdb -noh >1a6z_final.pdb</code> |
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* because there was no crystal water in the origin pdb included, we had nothing to concatenate. |
* because there was no crystal water in the origin pdb included, we had nothing to concatenate. |
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| + | '''Creation of the gromac files''' |
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| + | * <code>pdb2gmx -f 1a6z_final.pdb -o 1a6z_final.gro -p 1a6z_final.top -water tip3p -ff amber03 -vsite hydrogens</code> |
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Revision as of 12:19, 6 July 2011
Preparation
repairPDB 1a6z.pdb -ssw 15t >ssw.tmpbut there was no crystal water included.repairPDB 1a6z.pdb -nosol >1a6z_clean.pdbscwrl -i 1a6z_clean.pdb -s 1a6z_low.txt -o 1a6z_clean_complete.pdb > out.logrepairPDB 1a6z_clean_complete.pdb -noh >1a6z_final.pdb- because there was no crystal water in the origin pdb included, we had nothing to concatenate.
Creation of the gromac files
pdb2gmx -f 1a6z_final.pdb -o 1a6z_final.gro -p 1a6z_final.top -water tip3p -ff amber03 -vsite hydrogens
