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

-- From: "Dan Gil"; Date: Tue, Aug 14, 2018 04:39 AM To: "gmx-users"; Subject: Re: [gmx-users] No default Ryckaert-Bell. types Hello, This is telling you that the OPLS-AA force field does not have the dihedral force-field parameters for your molecule (topol_Other_chain_C.

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

Hello, This is telling you that the OPLS-AA force field does not have the dihedral force-field parameters for your molecule (topol_Other_chain_C.itp) of the Ryckaert-Bell type. Your exact problem might be: (1) There is something wrong with the molecule topology. (2) OPLS-AA really doesn't have

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

Dear All, I experienced an error as follows: (I used the OPLS-AA force field) ERROR 48600 [file topol_Other_chain_C.itp, line 144934]: No default Ryckaert-Bell. types Anyone can help? Kind regards, -- Dr. Baolin Huang Lecturer, School of Life Sciences, Guangzhou

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

On 9/3/15 7:19 AM, Daniele Veclani wrote: Dear Naga Rajesh Tummala I read in the manual the part relating to Ryckaert-Bell. angles. But I did not understand how to enter the 5 parameters. Do you tell me where I can find a guide? You enter the parameters with a text editor. The mechanics

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

Dear Naga Rajesh Tummala I read in the manual the part relating to Ryckaert-Bell. angles. But I did not understand how to enter the 5 parameters. Do you tell me where I can find a guide? Best regard 2015-09-02 18:02 GMT+02:00 Naga Rajesh Tummala : > In the dihedrals

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

Dear users. I'm trying to build the file .top for a molecule with opls FF. To do this I used MKTOP but when I run grompp I get this error: "ERROR 23 [file nor.top, line 227]: No default Ryckaert-Bell. types" This is my file .top: [ moleculetype ] ; Namenrexcl MOL 3

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

Thank you for your answer. how can I put these parameters in the .top file? Best regard. 2015-09-02 17:34 GMT+02:00 Naga Rajesh Tummala : > The parameters for the RB dihedral in line 227 are not described in the > opls forcefield. Either you can provide the parameters

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

The parameters for the RB dihedral in line 227 are not described in the opls forcefield. Either you can provide the parameters in your top file or include the dihedral paramters in the opls forcefield files tht comes with gromacs. On Wed, Sep 2, 2015 at 11:28 AM, Daniele Veclani

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

In the dihedrals section, similar to the bonds and angles section, the parameters are followed after the dihedral type.. 2 1 3 4 3 v0 v1 v2 v3 v4 v5 for RB type On Wed, Sep 2, 2015 at 11:48 AM, Daniele Veclani wrote: > Thank you for your answer. > > how can I put

Re: [gmx-users] No default Ryckaert-Bell. types for proline

On 6/3/15 12:00 AM, Kevin C Chan wrote: Thanks Justin, I have long been confused by atom names and types in Gromacs topology. I have just went through the manual again, and it confirms me that what we read directly in ffbonded.itp under GMXHOME/share/gromacs/top/oplsaa.ff are atomtypes. In

[gmx-users] No default Ryckaert-Bell. types for proline

Thanks Justin, I'm sorry that I'm not clear with what do you mean by so you can likely just use the same parameters in ffbonded.itp for this dihedral in the zwitterionic form. Also as I have mentioned before, when I look into the line 161, it refers to a dihedral term concerning (CD N CA C)

Re: [gmx-users] No default Ryckaert-Bell. types for proline

Thanks Justin, I have long been confused by atom names and types in Gromacs topology. I have just went through the manual again, and it confirms me that what we read directly in ffbonded.itp under GMXHOME/share/gromacs/top/oplsaa.ff are atomtypes. In other words, what you have listed in the last

Re: [gmx-users] No default Ryckaert-Bell. types for proline

On 6/1/15 12:25 PM, Kevin C Chan wrote: pdb2gmx command: gmx_d pdb2gmx -f proline.pdb -ter 15: (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) 1: TIP4P TIP 4-point, recommended 1: PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one residue) 1:

Re: [gmx-users] No default Ryckaert-Bell. types for proline

​Thanks Justin, I did not but I tried just now. The aforementioned dihedral terms ​remain along with the errors. Thanks in advance, Kevin On Mon, Jun 1, 2015 at 11:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/1/15 10:57 AM, Kevin C Chan wrote: Dear Users, I am testing with OPLSSaa

Re: [gmx-users] No default Ryckaert-Bell. types for proline

pdb2gmx command: gmx_d pdb2gmx -f proline.pdb -ter 15: (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) 1: TIP4P TIP 4-point, recommended 1: PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one residue) 1: PRO-ZWITTERION_COO- (only use with zwitterions containing

Re: [gmx-users] No default Ryckaert-Bell. types for proline

On 6/1/15 10:57 AM, Kevin C Chan wrote: Dear Users, I am testing with OPLSSaa force-field of proline. First I arbitrarily extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro and top are however not suitable for further grompp (even minimization). The error messages are as

Re: [gmx-users] No default Ryckaert-Bell. types for proline

On 6/1/15 12:09 PM, Kevin C Chan wrote: ​Thanks Justin, I did not but I tried just now. The aforementioned dihedral terms ​remain along with the errors. Please provide your full pdb2gmx command, all screen output, and full topology. Use file sharing services, pastebin, etc. as needed.

[gmx-users] No default Ryckaert-Bell. types for proline

Dear Users, I am testing with OPLSSaa force-field of proline. First I arbitrarily extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro and top are however not suitable for further grompp (even minimization). The error messages are as follows: ERROR 1 [file topol.top, line 161]: