[gmx-users] Grompp Error No default Ryckaert-Bell. types

Dear gromacs users. I am simulating a molecule in opls-aa force field. While running energy minimization I did get the error No default Ryckaert-Bell. types. I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO) has No default Ryckaert-Bell. types. but on checking

Re: [gmx-users] Grompp Error No default Ryckaert-Bell. types

On 7/10/15 9:47 AM, Anurag Dobhal wrote: Dear gromacs users. I am simulating a molecule in opls-aa force field. While running energy minimization I did get the error No default Ryckaert-Bell. types. I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO) has No default

[gmx-users] Grompp error No default Ryckaert-Bell. types

Hello all How can I address the No default Ryckaert-Bell. types error. The error is also in between the atoms which are not bonded with each other. Thank you -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever. Alex Thank you for your reply. I am simulating a PLGA (poly lactic co-glycolic acid molecle). I get the topology file and I solvated the molecule. my system is neutral.

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

"Which angles?" -- wait until Mark Abraham gets here. You must have a very special version of aminoacids.rtp Example: https://github.com/gromacs/gromacs/blob/master/share/top/gromos43a2.ff/aminoacids.rtp Thank you But which angles I need to add in .rtp file. are you talking about

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

The rtp file format and its acceptable entries are not forcefield-specific (oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to give an example of that. The oplsaa version of aminoacids.rtp only lists dihedral and improper angles explicitly, and that is exactly what's

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

On 5/4/15 4:20 AM, Alex wrote: The rtp file format and its acceptable entries are not forcefield-specific (oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to give an example of that. The oplsaa version of aminoacids.rtp only lists dihedral and improper angles

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

JL 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are JL required to define connectivity. Remaining bonded interactions are then deduced JL from bond connectivity. If a directive like [angles] or [dihedrals] is present, JL those values are used, instead. If an

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

On 5/4/15 1:06 PM, Alex wrote: JL 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are JL required to define connectivity. Remaining bonded interactions are then deduced JL from bond connectivity. If a directive like [angles] or [dihedrals] is present, JL those

Re: [gmx-users] Grompp error No default Ryckaert-Bell. types

True, thats why i mentioned Mark.:-) In all honesty, though, for small molecules, i would prefer to ignore the new format and actually add everything in the rtp entry to make ffbonded look like less of a zoo. Also, it was late night of extreme gromacs intercourse for me, which finally paid off.