Re: [gmx-users] CMAP format on GROMACS

On 1/8/20 10:25 AM, Marcelo Depólo wrote: Thanks for your input, Justin. Helpful as always. I am assuming the array is formatted to vary phi as a function of psi i.e. (-180,-180), (-180,-165), (-180,-150) [considering (phi,psi)] and again but for phi = -165. I am also assuming that, since

Re: [gmx-users] CMAP format on GROMACS

Thanks for your input, Justin. Helpful as always. I am assuming the array is formatted to vary phi as a function of psi i.e. (-180,-180), (-180,-165), (-180,-150) [considering (phi,psi)] and again but for phi = -165. I am also assuming that, since it is a 24x24 matrix, values will start in

Re: [gmx-users] CMAP format on GROMCACS

On 1/6/20 4:46 PM, Marcelo Depólo wrote: Hi everybody! Happy new year! =) I would like to understand a little bit better the CMAP format of charmm27.ff within GROMACS. I've looked up in the manual but found little information. I understand that it is defined by 5 atoms (1-4 phi and 2-5

[gmx-users] CMAP format on GROMCACS

Hi everybody! Happy new year! =) I would like to understand a little bit better the CMAP format of charmm27.ff within GROMACS. I've looked up in the manual but found little information. I understand that it is defined by 5 atoms (1-4 phi and 2-5 psi), a arbitrary identification number (e.g. 1)

Re: [gmx-users] cmap error while making tpr file from dcd file

Hi, XTC files don't have CMAP and grompp doesn't accept them as the main input. How exactly are you calling grompp to get such an error? The problem is likely related to the .top file. Mark On Thu., 13 Jun. 2019, 18:10 Santanu Santra, wrote: > hey users, > While I'm trying to

[gmx-users] cmap error while making tpr file from dcd file

hey users, While I'm trying to calculate some properties in gromacs from dcd files (NAMD), I followed the protocol in generating xtc file from vmd by loading psf and pdb files, and by grompp engine using a similar mdp file equivalent to my NAMD configuration file, I got CMAP error

Re: [gmx-users] CMAP TORSION ERROR

On 2/4/19 8:11 AM, Saman Fatihi wrote: Hi, I am working on a protein which i have modeled using Maestro. And usig charmm36 force field. I am facing a *unknown CMAP torsion while executing grompp and No proper default dihedral type error. * Could you please suggest how to correct this error

[gmx-users] CMAP TORSION ERROR

Hi, I am working on a protein which i have modeled using Maestro. And usig charmm36 force field. I am facing a *unknown CMAP torsion while executing grompp and No proper default dihedral type error. * Could you please suggest how to correct this error and the reason of it. I tried few things but

Re: [gmx-users] CMAP entries for D-residues with GROMACS (Justin Lemkul)

OK I see thank you, Justin Bye On 3/2/18 10:50 AM, ABEL Stephane wrote: > Dear all, > > I am interested to simulate a system with gramicidin A that contains D-AAs > (D-LEU and D-VaL) and I am wondering if the CMAP entries in the cmap.itp > file (charmm36-jul2017.ff) are used for these types

Re: [gmx-users] CMAP entries for D-residues with GROMACS

On 3/2/18 10:50 AM, ABEL Stephane wrote: Dear all, I am interested to simulate a system with gramicidin A that contains D-AAs (D-LEU and D-VaL) and I am wondering if the CMAP entries in the cmap.itp file (charmm36-jul2017.ff) are used for these types of AA ? I am asking this because I

[gmx-users] CMAP entries for D-residues with GROMACS

Dear all, I am interested to simulate a system with gramicidin A that contains D-AAs (D-LEU and D-VaL) and I am wondering if the CMAP entries in the cmap.itp file (charmm36-jul2017.ff) are used for these types of AA ? I am asking this because I see that the CHARMM force field library

Re: [gmx-users] cmap

On 11/26/17 6:33 PM, MD wrote: Hi Justin, I added the CSO to residuetypes.dat in my local computer and it worked now. I then tried to copy the modified "residuetypes.dat" to the ff folder on the server computer, but the server computer gromacs wouldn't give option to choose which

Re: [gmx-users] cmap

Hi Justin, I added the CSO to residuetypes.dat in my local computer and it worked now. I then tried to copy the modified "residuetypes.dat" to the ff folder on the server computer, but the server computer gromacs wouldn't give option to choose which residuetypes.dat to use. Do you know how to let

Re: [gmx-users] cmap

On 11/26/17 6:06 PM, MD wrote: Hi, I had to repost this cause of the size of the previous thread. I had another error after grompp, "ERROR 1 [file topol_Protein_chain_E.itp, line 52165]: Unknown cmap torsion between atoms 3022 3024 3026 3046 3049" The 3022 3024 3026 3046 3049 in the itp

[gmx-users] cmap

Hi, I had to repost this cause of the size of the previous thread. I had another error after grompp, "ERROR 1 [file topol_Protein_chain_E.itp, line 52165]: Unknown cmap torsion between atoms 3022 3024 3026 3046 3049" The 3022 3024 3026 3046 3049 in the itp files referred to the backbone

Re: [gmx-users] CMAP missing for a new residue.

It seems to work :). Thank you! 2015-09-04 9:52 GMT+01:00 Dawid das : > > 2015-09-03 13:06 GMT+01:00 Justin Lemkul : > >> FYI, CHARMM22 has no CMAP. CHARMM22/CMAP (what GROMACS somewhat >> misleadingly calls "charmm27.ff") does. >> > Yes, I was aware of

Re: [gmx-users] CMAP missing for a new residue.

2015-09-03 13:06 GMT+01:00 Justin Lemkul : > FYI, CHARMM22 has no CMAP. CHARMM22/CMAP (what GROMACS somewhat > misleadingly calls "charmm27.ff") does. > Yes, I was aware of that, just forgot to write CHARM22/CMAP. > > My question is, whether there is a way to use CMAP

[gmx-users] CMAP missing for a new residue.

Dear Gromacs Experts, I am working with fluorescent protein, posesing a chromophore which I defined as a non-standard " amino-acid residue". Now, I want to use Charmm22 force field and the issue is that I am missing CMAP parameters and these are not available in the literature. My question is,

Re: [gmx-users] CMAP missing for a new residue.

On 9/3/15 3:42 AM, Dawid das wrote: Dear Gromacs Experts, I am working with fluorescent protein, posesing a chromophore which I defined as a non-standard " amino-acid residue". Now, I want to use Charmm22 force field and the issue is that I am missing CMAP parameters and these are not