Re: [gmx-users] Adding a new residue and Duplicate atom index () in angles error

2019-10-04 Thread Justin Lemkul
On 10/3/19 8:57 PM, Mijiddorj B wrote: Dear Justin, Thank you very much for your prompt response. Do you mean that I made a mistake when I define the bonds in .rtp file? Yes. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor

Re: [gmx-users] Adding a new residue and Duplicate atom index () in angles error

2019-10-03 Thread Mijiddorj B
Dear Justin, Thank you very much for your prompt response. Do you mean that I made a mistake when I define the bonds in .rtp file? Best regards, Mijiddorj > -- > > Message: 6 > Date: Thu, 3 Oct 2019 15:47:13 -0400 > From: Justin Lemkul > To: gmx-us...@gromacs.org

Re: [gmx-users] Adding a new residue and Duplicate atom index () in angles error

2019-10-03 Thread Justin Lemkul
On 10/3/19 11:56 AM, Mijiddorj B wrote: Dear GMX experts, I am trying to prepare CHARMM36 parameter for non-standard amino acid using some instructions such as http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field and the user manual. After I modified merged.rtp,

[gmx-users] Adding a new residue and Duplicate atom index () in angles error

2019-10-03 Thread Mijiddorj B
Dear GMX experts, I am trying to prepare CHARMM36 parameter for non-standard amino acid using some instructions such as http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field and the user manual. After I modified merged.rtp, merged.hdb, and residuetype.data files,