Re: [gmx-users] top/itp file to show parameters explicitly

2012-05-23 Thread Alan
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

Re: [gmx-users] top/itp file to show parameters explicitly

2012-05-23 Thread Mark Abraham
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

Re: [gmx-users] top/itp file to show parameters explicitly

2012-05-22 Thread Alan
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

Re: [gmx-users] top/itp file to show parameters explicitly

2012-05-22 Thread Justin A. Lemkul
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

Re: [gmx-users] top/itp file to show parameters explicitly

2012-05-21 Thread Justin A. Lemkul
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