Re: [gmx-users] Error from residues added to rtp file

Dear Gromacs users, I am once again requesting your help for the editing of the opls force field .rtp and .hdb files. I have inserted the parameters for a new residue, N-methyl methionine (MME). In this molecule, the methyl group is attached to the nitrogen atom from the peptide bond, which

Re: [gmx-users] Error from residues added to rtp file

On 5/09/2011 6:41 PM, Delmotte, Antoine wrote: Dear Gromacs users, I am once again requesting your help for the editing of the opls force field .rtp and .hdb files. I have inserted the parameters for a new residue, N-methyl methionine (MME). In this molecule, the methyl group is attached to

Re: [gmx-users] Error from residues added to rtp file

This solved my problem, although I am not totally sure to have perfectly understood how the .tdb had to be edited. I added the following entry: [ MME-NH ] [ delete ] H Anyway, it solved the problem I had. Many thanks for your help! Antoine On 09/05/2011 09:54 AM, Mark Abraham wrote: On 5/09

[gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27

I want to make a model of a GPCR inserted into lipid bilayer. I obtained the structure file for a solvated POPC bilayer from the CHARMM-GUI site. I used CHARMM27 force field to model the bilayer and *pdb2gmx *had no problem generating the *.gro, *.top, and posre.itp files. When I perform *grompp

Re: [gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27

Jackson Chief wrote: I want to make a model of a GPCR inserted into lipid bilayer. I obtained the structure file for a solvated POPC bilayer from the CHARMM-GUI site. I used CHARMM27 force field to model the bilayer and *pdb2gmx *had no problem generating the *.gro, *.top, and posre.itp fi

Re: [gmx-users] Question about adding hydrogens to a newly constructed residue

On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham wrote: > On 5/09/2011 3:30 AM, J. Nathan Scott wrote: > >> Hello fellow GROMACS users, >> >> I am in the process of constructing a new residue in the OPLS-AA force >> field for the mCherry chromophore. However, I am having some difficulty in >> adding

Re: [gmx-users] Question about adding hydrogens to a newly constructed residue

On 6/09/2011 1:22 AM, J. Nathan Scott wrote: On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham > wrote: On 5/09/2011 3:30 AM, J. Nathan Scott wrote: Hello fellow GROMACS users, I am in the process of constructing a new residue in the O

Re: [gmx-users] Question about adding hydrogens to a newly constructed residue

On Mon, Sep 5, 2011 at 9:29 AM, Mark Abraham wrote: > On 6/09/2011 1:22 AM, J. Nathan Scott wrote: > > > > On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham wrote: > >> On 5/09/2011 3:30 AM, J. Nathan Scott wrote: >> >>> Hello fellow GROMACS users, >>> >>> I am in the process of constructing a new r

[gmx-users] Half double pair list method in GROMACS [update]

Dear All, Below a little update and results about the application of half double pair list method to scale properly the Coulombic 1-4 interactions in case of a system where the AMBER99SB (fudgeLJ=0.5 and fudgeLJ=0.8333) and GLYCAM06 (fudgeLJ=1.0 and fudgeLJ=1.0) force fields are combined. I ha

[gmx-users] problem in topology with AMBER99SB

Dear gmx-users, I'm trying to create the topology for a ligand using Amber99SB force field, but I'm experimenting several problems. Here what I did: - I recovered the .mol2 file of my ligand (comp1.mol2) - I checked and added H with Amber tool reduce: reduce comp1.mol2 > comp1-H. mol2 - I added ch

Re: [gmx-users] problem in topology with AMBER99SB

Anna Marabotti wrote: Dear gmx-users, I'm trying to create the topology for a ligand using Amber99SB force field, but I'm experimenting several problems. Here what I did: - I recovered the .mol2 file of my ligand (comp1.mol2) - I checked and added H with Amber tool reduce: reduce comp1.mol2

[gmx-users] Counting number of non-bonded interactions ?

Hi Is there any function to count number of non-bonded interactions with Gromacs ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting

[gmx-users] Deuterium order parametr

Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the angle between the bilayer normal and the -C

Re: [gmx-users] Deuterium order parametr

Parthasarathi, Ramya wrote: Hi, I am trying to write a code for Deuterium order parameter of DOPC lipid. I went through the code in gmx_order.c, I did the following, 1. I took the carbons in the chain, and found its neighbors. 2. Took the bilayer normal and found the ang

RE: [gmx-users] Deuterium order parametr

Sorry did not send the email.. was sent by mistake due to some error in the mail box. I apologise.. Ramya -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, September 05, 2011 12:49 PM To: Discussion l

Re: [gmx-users] REMD Error

Hi Mark, I just posted a bug on redmine for the remd problem that I encountered. I was as thorough as possible about how to recreate the bug, but if I forgot some crucial piece of information let me know and I will get it to you as soon as possible. Thanks for your time. Jose Tusell On Sat, Se

Re: [gmx-users] Counting number of non-bonded interactions ?

On 6/09/2011 3:40 AM, Chih-Ying Lin wrote: Hi Is there any function to count number of non-bonded interactions with Gromacs ? Before or after cut-offs? Interaction types or actual interactions? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listin

Re: [gmx-users] Question about adding hydrogens to a newly constructed residue

On 6/09/2011 1:44 AM, J. Nathan Scott wrote: On Mon, Sep 5, 2011 at 9:29 AM, Mark Abraham > wrote: On 6/09/2011 1:22 AM, J. Nathan Scott wrote: On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote: On 5/09

[gmx-users] atom type OXT

Hi all, I have been trying to pdbgmx my protein to obtain the gro and top files as follows: pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top -ter -ignh However, I get an error message that states: Atom OXT in residue SER 29 was not found in rtp entry SER with 8 atoms while sorting atoms I f

Re: [gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27

Why not use CHARMM36 FF? It is available in gromacs user contribution website. If I remember correctly, charmm27 cannot yield correct area/lipid, you need to apply surface tension. Cheeers, Jianguo From: Jackson Chief To: gmx-users@gromacs.org Sent: Monday, 5