You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever.
Alex
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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. while running the grompp I got 6 No default Ryckaert-Bell. types. I rechecked my parameters in .rtp file and I found them correct, or may be I am unable to found the problem. I am using ions.mdp file which is given in the tutorial (lysozyme tutorial). I have attatched the .pdb file and the .rtp parameters for them. can you please check the parameters which I have given. so that I can rectify the errors. awaiting for your reply. Best Anurag Dobhal Juniour Research fellow Supervisor: Dr. Ratnesh D. Jain Department of chemical engineering Insttute of Chemical Technology 400019, +91 8898486877 On Mon, May 4, 2015 at 12:11 PM, Alex <nedoma...@gmail.com> wrote: It may sound surprising, but this is resolved by either introducing correct R-B term parameters in your topology/ff definitions, or by removing the mess from the input coordinates, especially when non-bonded atoms are determined to participate in a dihedral. Humor aside, more information about the system is needed. Alex AD> Hello all AD> How can I address the "No default Ryckaert-Bell. types error". AD> The error is also in between the atoms which are not bonded with each other. AD> Thank you AD> -- AD> *DISCLAIMER:* AD> *This communication is intended only for the person or entity to which it AD> is addressed and may contain confidential and / or privileged material. Any AD> review, retransmission, dissemination or other use is prohibited. If you AD> have received this in error, please contact the sender and delete this AD> material from your computer. Kindly note that this mail does not constitute AD> an offer or solicitation for the purchase or sale of any financial AD> instrument or as an official confirmation of any transaction. The AD> information is not warranted as to completeness or accuracy and is subject AD> to change without notice. Any comments or statements made herein do not AD> necessarily reflect those of Nanomedicine Research Group. Before opening AD> the email or accessing any attachments, please check and scan for virus.* DISCLAIMER: This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus. |
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Best regards,
Sasha mailto:nedoma...@gmail.com
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