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 cross-referenci
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 wrote:
>
>
> On 5/22/12 12:46 PM, Alan wrote:
>
>> Hi Justin, your suggestion got close. However, let me give an example.
>
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
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 a
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 4
The actual parameters are listed in the ffbonded.itp file located in the
folder of the corresponding force field, under [ dihedraltypes ] section.
Javier
El 21/05/12 14:43, Alan escribió:
Hi there,
Is there an option in pdb2gmx that when generating the top/itp file,
it could show the paramet
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