Re: [gmx-users] dssp doubt

Hi Justin, Thank you for your descriptive reply. I prepared new index.file which includes mainchain, and when I used the do_dssp with -n index.ndx, it worked. But, if I doesn't use the index file, again, the "Protein" is selected by the system. It is weird.. Best regards, Deniz On Thu, Jun 7, 2

Re: [gmx-users] N-terminus problem

Hi Mark, Thank you for your reply. Let me explain the problem a little more and answer your questions. I would be happy if you could expound upon your reply. Hi Gromacs users, I created a lipopeptide (lauroic acid connected to an 8-residue peptide > which starts with Valine). > > How

[gmx-users] N-terminus problem

Hi Gromacs users, I created a lipopeptide (lauroic acid connected to an 8-residue peptide which starts with Valine). · If I try to use pdb2gmx with -ter flag (Start terminus VAL-2: None, End terminus ASP-9: COO-), everything seems to work (topology is created.). · But, if I t

[gmx-users] Atom OXT in residue ASP 18 was not found in rtp entry ASP with 9 atoms while sorting atoms.

Hi all, I wrote a own code to put three identical lipopeptide at desired positions. Then I used the pdb2gmx with –ter flag to get the system’s topology, I have encountered the following error: Fatal error: Atom OXT in residue ASP 18 was not found in rtp entry ASP with 9 atoms while sorting at

[gmx-users] strain

Hi Gromacs users, We would like to apply strain to the system. Is this possible to do with gromacs and if it is how? Thank you in advance, Deniz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromac

[gmx-users] gen-pairs

Hi gromacs users, I wish to simulate a system using the Gromos53a6 force field. When I try to run, I get the following errors: ERROR 1 [file topol.top, line 194]: No default LJ-14 types ERROR 2 [file topol.top, line 195]: No default LJ-14 types ERROR 3 [file topol.top, line 198]: No defau

Re: [gmx-users] aminoacids.n.tdb

rk Abraham wrote: > On 12/04/2011 10:30 PM, Emine Deniz Tekin wrote: > > > Hi Mark, > > > Thank you for your reply. But, I couldn’t understand very well what you > meant “you can make one that uses backbone-style linking. Most of the > forcefields will have examples o

Re: [gmx-users] aminoacids.n.tdb

Mark Abraham wrote: > On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote: > >> >> Hi Gromacs users, >> >> I want to covalently link the lauroic acid to the Valine residue (it is a >> peptide (amide) bond), I know that I should update the specbond.dat.But >> b

[gmx-users] aminoacids.n.tdb

Hi Gromacs users, I want to covalently link the lauroic acid to the Valine residue (it is a peptide (amide) bond), I know that I should update the specbond.dat. But before updating this file, I need the NH as an N terminal of the first residue (Valine). When I used pdb2gmx with the –ter flag,

Re: [gmx-users] lipopeptide problem

it. Lecturing me on "willingness" is crossing the line. How do you know how much I tried? Anyhow, thanks for your earlier help, but you can simply skip my future postings. Best regards, Deniz On Thu, Mar 17, 2011 at 12:00 AM, Justin A. Lemkul wrote: > > > Emine Deniz T

[gmx-users] lipopeptide problem

Hi GROMACS Users, I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I simulated a peptide before but this is the first time I am trying to combine a lipid with a peptide (to get a lipo-peptide). I would be really happy if you could help me out with the following question I am trin

[gmx-users] DENIZ-senin yapacagina benzer birsey yapmis, residue eklemis..

On Fri, Mar 4, 2011 at 9:13 AM, Mark Abraham wrote: > On 3/03/2011 11:42 PM, Justin A. Lemkul wrote: > >> >> >> bharat gupta wrote: >> >>> The residue is a chromophore of Green Fluorescent Protein. The parameter >>> file that I have got has the connection for serine and glycine :- >>> >>> >> For t

Re: [gmx-users] Residue 'DEF' not found in residue topology database

A. Lemkul wrote: > > > Emine Deniz Tekin wrote: > >> >> Hi gromacs users, >> >> >> I am using the gromacs 4.5.3 version. I created a lipopetide which consist >> of 12 Carbon atoms (tail) connected to Val-Val-Ala-Gly-Glu-Arg-Gly-Asp >> (residues)

Re: [gmx-users] Website search broken

Hi Justin, No matter what I search at gromacs search field, it gives the same error message. Deniz On Wed, Feb 23, 2011 at 3:58 PM, Justin A. Lemkul wrote: > > Hi, > > Is anyone else having problems using the search feature on the Gromacs > site? If I search for "tutorials," I get: > > Your ad

[gmx-users] Residue 'DEF' not found in residue topology database

Hi gromacs users, I am using the gromacs 4.5.3 version. I created a lipopetide which consist of 12 Carbon atoms (tail) connected to Val-Val-Ala-Gly-Glu-Arg-Gly-Asp (residues) using ARGUSLAB and I saved it as a pdb file. Then, when I used the following command in gromacs: pdb2gmx –flipope