Re: [gmx-users] ligand parameters (was Re: gmx-users Digest, Vol 79, Issue 114)

Two notes before the comments below: 1. Please do not copy an entire digest message. It makes the archiving process and list searching unnecessarily complicated. 2. Choose an appropriate subject line, especially when introducing a new topic. ITHAYARAJA wrote: Dear Sir, Greetings! It may b

Re: [gmx-users] Ligand Parameters

Thanks to all for sharing thoughts. I will keep the list apprised of any successes; it may be useful to others down the road. -Justin Quoting FyD <[EMAIL PROTECTED]>: > Quoting Justin Lemkul <[EMAIL PROTECTED]>: > > > I am interested in simulating some small molecules that involve oxygen in > >

Re: [gmx-users] Ligand Parameters

Quoting Justin Lemkul <[EMAIL PROTECTED]>: I am interested in simulating some small molecules that involve oxygen in aromatic rings (which thus bears a +1 charge). I tried to submit one of these molecules to PRODRG, but got an error indicating that there were too many bonds to O. I thou

Re: [gmx-users] Ligand Parameters

David Mobley wrote: Justin, I have also considered submitting an analog of my compound to PRODRG (normal aromatic ring instead of one containing O+) to get the dihedrals, etc. and then re-calculating charges under ANTECHAMBER. Any thoughts on that approach? Presumably dihedrals, etc are af

Re: [gmx-users] Ligand Parameters

David, Thank you for the quick and detailed reply. I thought that the analog approach would be a bit too quick-and-dirty, anyway :-) I will set to work on making some new parameters based on the information you've provided, and I will likely focus on compatibility with the GROMOS force fields.

Re: [gmx-users] Ligand Parameters

Justin, I am interested in simulating some small molecules that involve oxygen in aromatic rings (which thus bears a +1 charge). I tried to submit one of these molecules to PRODRG, but got an error indicating that there were too many bonds to O. I thought this issue might arise, due to the unu

[gmx-users] Ligand Parameters

Hello all, I am interested in simulating some small molecules that involve oxygen in aromatic rings (which thus bears a +1 charge). I tried to submit one of these molecules to PRODRG, but got an error indicating that there were too many bonds to O. I thought this issue might arise, due to the un