Thanks Justin, you were right. In the end gmxdump helped to clear some
doubts but I wished it would be less painfully.
Cheers,
Alan
On 22 May 2012 12:36, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/22/12 12:46 PM, Alan wrote:
Hi Justin, your suggestion got close. However, let me give an
On 23/05/2012 6:42 PM, Alan wrote:
Thanks Justin, you were right. In the end gmxdump helped to clear some
doubts but I wished it would be less painfully.
One useful approach is to simplify the system as much as possible before
producing the .tpr and using gmxdump. The necessary
Hi Justin, your suggestion got close. However, let me give an example. You
can use the Gly-Gly-Gly example I am attaching and do this:
pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top -water none
/sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr -pp aGGGp.top
if you look
On 5/22/12 12:46 PM, Alan wrote:
Hi Justin, your suggestion got close. However, let me give an example. You can
use the Gly-Gly-Gly example I am attaching and do this:
pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top -water none
/sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o
On 5/21/12 2:43 PM, Alan wrote:
Hi there,
Is there an option in pdb2gmx that when generating the top/itp file, it could
show the parameters explicitly? e.g.:
Instead of:
[ dihedrals ]
; aiajakal functc0c1c2
c3
5131112
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