[gmx-users] Incorrect number of parameters

Dear Gmx Users, I run the simulation of protein-ligand complex. Then I extracted coordinates for SMD - I want to pull away my ligand. I used to topology from pevious simulation, so I removed water, ions from topol.top as the size box will be changed etc. I placed protein-ligan in new box and

Re: [gmx-users] Incorrect number of parameters

On 3/05/2012 8:08 PM, Steven Neumann wrote: Dear Gmx Users, I run the simulation of protein-ligand complex. Then I extracted coordinates for SMD - I want to pull away my ligand. I used to topology from pevious simulation, so I removed water, ions from topol.top as the size box will be

[gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q

Dear GROMACS users, I am beginner to GROMACS. I want to simulate my protein in different concentrations of Guanidinium Chloride solution and collected the files (3M 5M box and .itp file) from http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies. Then I build a topology file

Re: [gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q

Biswajit Gorai wrote: Dear GROMACS users, I am beginner to GROMACS. I want to simulate my protein in different concentrations of Guanidinium Chloride solution and collected the files (3M 5M box and .itp file) from http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies.

Re: [gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q

Dear Lemkul, Thanks. Can any one suggest how/where to get the correct .itp file for Guanidinium Chloride? Regards Biswajit On Tue, Mar 20, 2012 at 5:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: Biswajit Gorai wrote: Dear GROMACS users, I am beginner to GROMACS. I want to simulate my

Re: [gmx-users] Incorrect number of parameters - found 2, expected 5 or 5 for LJC-14 q

Biswajit Gorai wrote: Dear Lemkul, Thanks. Can any one suggest how/where to get the correct .itp file for Guanidinium Chloride? It should be straightforward to modify the existing file. FudgeQQ is fixed for a given force field, qi and qj are given in the topology itself, and

[gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.

Dear justin, I have made the itp file on a basis of chapter 5 of gromacs. Every things seems fine. my itp file for opls is as follow: ; [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 opls_185 1 DRG HAD 1

Re: [gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.

Morteza Khabiri wrote: Dear justin, I have made the itp file on a basis of chapter 5 of gromacs. Every things seems fine. my itp file for opls is as follow: Seems fine is your own evaluation, but if grompp is giving you errors about an incorrect topology, then indeed it is not. Did

[gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.

Dear Justin, thanks for your help. The last lines of my grompp are: checking input for internal consistency... calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4

Re: [gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.

* Justin A. Lemkul [EMAIL PROTECTED] [2008-09-10 05:46:07 -0400]: Morteza Khabiri wrote: Dear justin, I have made the itp file on a basis of chapter 5 of gromacs. Every things seems fine. my itp file for opls is as follow: Seems fine is your own evaluation, but if grompp is giving you

Re: [gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.

Morteza Khabiri wrote: Dear Justin, thanks for your help. The last lines of my grompp are: checking input for internal consistency... calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated