[gmx-users] looking for polar lipid pdb

Grateful for receiving DOPC.pdb file thanks francesco pietra -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list

Re: [gmx-users] Last step before CG em.mdp

ater. > > I mean in the top file you'll find the reference to the martini??.itp file > where the water is defined. >> >> On Dec 1, 2009, at 6:26 PM, Francesco Pietra wrote: >> >>> I forgot to ask, in additio to below, where to find the .itp file for >>&g

Fwd: [gmx-users] Last step before CG em.mdp

I forgot to ask, in additio to below, where to find the .itp file for cg water. All that I have is water.gro water.mdp water.top from the martini web site. -- Forwarded message -- From: Francesco Pietra Date: Tue, Dec 1, 2009 at 6:15 PM Subject: Re: [gmx-users] Last step before

Re: [gmx-users] Last step before CG em.mdp

On Mon, Nov 30, 2009 at 5:51 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> cpp                 =  /usr/bin/cpp >> define              =  -DFLEX_SPC > > You're using SPC water in a coarse grain model?  This doesn't make sense to > me - a

Re: [gmx-users] Fwd: Last step before CG em.mdp

On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Failed to specify that both the DPPC bilayer and the box of water are >> from equilibrated systems in MARTIN web, while the protein was Amber >> minimized (and MD) befor

[gmx-users] Fwd: Last step before CG em.mdp

ded message -- From: Francesco Pietra Date: Mon, Nov 30, 2009 at 5:36 PM Subject: Last step before CG em.mdp To: Discussion list for GROMACS users Hi: This is to ask how to proceed to minimize a CG ensemble made of a transmembrane multimer with pore region immersed in a hydrated DPPC bila

[gmx-users] Last step before CG em.mdp

francesco pietra -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users

[gmx-users] does editconf follow pdb rules?

cedure. My system treats differently W at 18 or 20 column and my explain the problems posted a couple of days ago in reply to demands by Justin. Thanks for checking francesco pietra -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] converting all-atom pdb to cg.pdb

would also be appreciated because one normally trusts in what is officially posted. thanks francesco pietra On Mon, Nov 9, 2009 at 12:58 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Does the atom2cg_v2.1.awk require the indication of the subunit (A, B, >&

[gmx-users] converting all-atom pdb to cg.pdb

residue numbers in the cg file are correct. I don't see any other difference between the two starting files. Or should I look for a different cause. thanks francesco pietra ... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please s

Fwd: Fwd: [gmx-users] scripts to generate topology CG

I was asked to submit details of the procedure to get a solvated CG system in order to see if help to correct the procedure is feasible. Is the described procedure still insufficient? thanks for answering francesco -- Forwarded message -- From: Francesco Pietra Date: Sun, Oct 25

Re: Fwd: [gmx-users] scripts to generate topology CG

On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: > >>> grep W solvated.gro | wc -l >>> >>> and use that number in the topology? >> >> I forgot to add that the graphic program uses the above grep command, >

Fwd: [gmx-users] scripts to generate topology CG

-- Forwarded message -- From: Francesco Pietra Date: Fri, Oct 23, 2009 at 5:01 PM Subject: Re: [gmx-users] scripts to generate topology CG To: jalem...@vt.edu, Discussion list for GROMACS users On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul wrote: > > > Frances

Re: [gmx-users] scripts to generate topology CG

On Fri, Oct 23, 2009 at 4:14 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Hello Sunny: >> I had already generated a valid .itp file for my protein using >> seq2itp. That .itp works for both the protein itself and the protein >> graphica

Re: [gmx-users] scripts to generate topology CG

without putting it everywhere. That script does not help. thanks francesco On Wed, Oct 21, 2009 at 3:46 PM, sunny mishra wrote: > There is a seq2itp.pl script provided by martini folks in their > website. You can get it from there. > > Sunny > > On Wed, Oct 21, 2009 at 9:42 AM

[gmx-users] scripts to generate topology CG

Hi: I am looking for scripts that generate topology in coarse grained. Thanks for indications. francesco pietra ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] top file in coarse-grained

ms in AMBER. thanks francesco On Mon, Oct 19, 2009 at 8:34 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Hi: >> >> As I meet recurring problems in coarse-grained of the top file not >> matching the number of coordinates in coordinate f

[gmx-users] top file in coarse-grained

Hi: As I meet recurring problems in coarse-grained of the top file not matching the number of coordinates in coordinate file, is there any way to get the top file automatically like in all-atoms? Editing the top file to this regard proved difficult in my hands. thanks francesco pietra

Re: [gmx-users] LAM OpenMPI conflict?

ed openmpi, no need to mention lam in the md command line. Forget about the Debian compilation, it does not require any special command. Have a nice day francesco On Thu, Oct 15, 2009 at 7:55 PM, Jussi Lehtola wrote: > On Thu, 2009-10-15 at 18:23 +0200, Francesco Pietra wrote: >>

Re: [gmx-users] LAM OpenMPI conflict?

On Thu, Oct 15, 2009 at 7:55 PM, Jussi Lehtola wrote: > On Thu, 2009-10-15 at 18:23 +0200, Francesco Pietra wrote: >> Hi: I was trying to minimize in vacuum a pure CG protein on a four >> core (two dual operons), getting errors: >> >> $ lamboot >> >&g

[gmx-users] LAM OpenMPI conflict?

in a quite different directory. "which" calls either parallelization support independently. Do the above error messages really imply a conflict LAM OpenMPI or should I better look at elsewhere? thanks francesco pietra ___ gmx-users mailing l

Re: [gmx-users] grompp: no such moleculetype

On Wed, Oct 14, 2009 at 7:22 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Hi Justin: >> Back from the Austrian mountains, to further isolate problems I >> encountered before with my protein, I have tried to reproduce - at the >> lowes

Re: [gmx-users] grompp: no such moleculetype

o "HOH" around in such file. Also, the tutorial was not for other non-protein. I would be very grateful to the kind person who points out where I did wrongly. Attached is also the mdout.mdp file. thanks francesco pietra On Mon, Oct 5, 2009 at 11:14 PM, Justin A. Lemkul wrote:

Re: [gmx-users] grompp: no such moleculetype

On Mon, Oct 5, 2009 at 8:20 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: > >> I have now used protein-in-vacuum.mdp from the ubiquitin cg tutorial. > > Which tutorial is that?  Can you provide a link? http://md.chem.rug.nl/~marrink/coarsegrain.html > >

Re: [gmx-users] grompp: no such moleculetype

On Mon, Oct 5, 2009 at 7:31 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> On Mon, Oct 5, 2009 at 4:39 PM, Justin A. Lemkul wrote: >>> >>> Francesco Pietra wrote: >>>> >>>> Thanks, and beg pardon for the pedestrian m

Re: [gmx-users] grompp: no such moleculetype

On Mon, Oct 5, 2009 at 4:39 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Thanks, and beg pardon for the pedestrian mistake. >> >> However, I am not yet out. .tpr not generated >> >> With command >> >> $ grompp -np

Re: [gmx-users] grompp: no such moleculetype

ompp, VERSION 3.3.3 Source code file: ../../../../src/gmxlib/futil.c, line: 345 File input/output error: index.ndx == Non-matching because of the many -S-S- bonds? Why asking about index.ndx? Thanks for help francesco On Mon, Oct 5, 2009 at 12:33 PM, Justin A. Lemkul wrote: > > > Fr

[gmx-users] grompp: no such moleculetype

ect to atom names, though I do not understand the error message above. Thanks for help francesco pietra ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs

[gmx-users] solvating a protein-bilayer CG assembly

DPP, W, Protein, so that the coordinates for new solvent will not change with the name. I feel I silly entered a mental loop. There must be in GROMACS commands to accomplish external solvation of an ensemble. Thanks and sorry for the length, probably a residue from the mentioned loop. f

[gmx-users] integration protein-bilayer in CG

machine. Thanks for help francesco pietra ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subs

[gmx-users] About a "general" force field

fatty acids,. or the like) in gromacs. As I am familiar with ab initio on NWChem, I could get parameters from ab initio, though generally it would be too time consuming for my type of interests. Thanks francesco pietra ___

Re: [gmx-users] gromacs-antechamber-gaff

window (without "s"). Cheers francesco pietra --- David Mobley <[EMAIL PROTECTED]> wrote: > David, > > On 5/18/07, David van der Spoel > <[EMAIL PROTECTED]> wrote: > > Francesco Pietra wrote: > > > Planning to use gromacs aided by > antech

[gmx-users] antechamber installation

monitoring. Thanks francesco pietra TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/ ___ gmx-users mailing list

[gmx-users] gromacs-antechamber-gaff

above seem inescapable problems/obstacles to me for accessing gromacs. Thanks francesco pietra Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. http://advision.webevents

Re: [gmx-users] atom types @ bonded parameters

. Thanks francesco --- David van der Spoel <[EMAIL PROTECTED]> wrote: > Francesco Pietra wrote: > > New to the list, aimed at installing gromacs on > Linux > > Debian amd64 dual-core-opterons for parallel > > execution, I would appreciate indications where > (not >

[gmx-users] atom types @ bonded parameters

equipped of QM suites and have also some experience with classical MD. My problem was always lack of bonded parameters and atom types that I need for my studies. Thanks francesco pietra (This is a project of mine of long date, and I also had exchange of emails with the Debian gromacs maintainer