Re: [gmx-users] Amino acid simulation
It's highly unusual to simulate a single amino acid. I don't exactly know what's your purpose with it, but if you really want to do it, you need to generate those parameters. I know there are web services for generating gromos FF parameters for "unusual" molecules, possibly there are such resources for amber or opls too. On Mon, Apr 12, 2010 at 8:36 PM, Chandan Choudhury wrote: > Hello gmx-users > > I am trying to simulate an amino acid (say GLN). It can be as a > zwitterionic form or uncharged ends. Neither ffamber or ffopls force fields > has a complete parameter for them. While in ffamber, I have the parameters > for CGLU and NGLU, but not for a Glutamine. Do I need to define it there, or > there is some way out. If I need to define it, how do I retrive the partial > charges. > > Any insight would be very helpful. > Thanks > > Chandan > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > -- > 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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] System has non-zero total charge: -8.000001e+00
You should always neutralise your sysem. On Thu, Feb 25, 2010 at 1:42 PM, Maurício Menegatti Rigo < mauriciomr1...@gmail.com> wrote: > IS this a problem? > > *System has non-zero total charge: -8.01e+00* > > If yes, can I fix that changing COulomb cutt-off to PME electrostatics? > > THanks!! > > -- > 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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] genbox
Can I define the maximum number of water molecules to be added by genebox.On 10/29/06, Mark Abraham <[EMAIL PROTECTED] > wrote:Tamas Horvath wrote:> Is it possible to maximise the water molecules to be inserted into the box? Define maximise.Mark___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] genbox
Is it possible to maximise the water molecules to be inserted into the box? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] special molecule
Does it mean, that the itp file, generated by the PRODRG server should only used with the gmx forcefield, or may it be combined with the other gromos frocefields, like the G43a2?On 6/13/06, Mark Abraham <[EMAIL PROTECTED]> wrote: Dongsheng Zhang wrote:> Sear Mark,>> Since PRODRG server only generates a itp file by using gromos type force> field, do I have to use gromos force field for my whole protein-ligand> system if my ligand force field parameters are got from PRODRG? In > another word, can I mix two different force field (one for protein, one> for ligand) in one system? Thanks!It's technically possible, if fiddly, but I'd strongly advise againstit. Force fields are mathematical constructs that are optimized to produce reasonable model physics as an interacting unit. There is noreason to suppose that a bond stretching parameter is a measure of bondstrength, for example, because the other parameters in this force field might have some quirk that this parameter is compensating for because ofthe optimization procedure. A force field is merely a point in ahigh-dimensional space which when used the right way has been shown to produce a useful physical model. Thus there is no reason to suppose thata few of those high-dimensional space coordinates plus some others fromsome other force field will combine to produce a useful physical model. Mark___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] special molecule
What I asked is, if I have to reorganise the pdb file, or renumber the residues, etc.On 6/13/06, Mark Abraham < [EMAIL PROTECTED]> wrote:Tamas Horvath wrote:> So if I generate an .itp with PRODRG, and link it in the .top file, then > grompp can use the original .pdb file? Or it's not that simple?The order of the [ molecules ] section will have to correspond to theorder in the structure file you supply with -c to grompp, but if you read the grompp manpage it is obvious that the format of that structurefile is irrelevant.Mark___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] special molecule
So if I generate an .itp with PRODRG, and link it in the .top file, then grompp can use the original .pdb file? Or it's not that simple?On 6/12/06, Alan Dodd
<[EMAIL PROTECTED]> wrote:It's entirely possible to mix and match forcefield
files to create a hybrid forcefield - the lipidforcefield I use has OPLS parameters for theheadgroups, custom parameters for lipid tails, and GMXparameters for everything else. As long as the hybridforcefield is internally consistent, it will work.
How accurate it is, is another matter...So yes, you can technically use PRODRG itps with otherforcefields, but bear in mind firstly, atomtypes etcin your itp file will all need checking to make surethey are accounted for in both forcefields (are
'default' values the same in one forcefield asanother, for instance? Probably not - you may need toalter the itp to describe defaults explicitly), andsecondly that they are not designed to be used in the
same system.--- Dongsheng Zhang <[EMAIL PROTECTED]>wrote:> Sear Mark,>> Since PRODRG server only generates a itp file by
> using gromos type force> field, do I have to use gromos force field for my> whole protein-ligand> system if my ligand force field parameters are got> from PRODRG? In> another word, can I mix two different force field
> (one for protein, one> for ligand) in one system? Thanks!>>> Best Wishes!>> Dongsheng>>>> On Tue, 2006-06-13 at 01:16 +1000, Mark Abraham> wrote:
> > Tamas Horvath wrote:> > > As I understand, if there are "special"> molecules in a pdb file, pdb2gmx> > > cannot convert it. However, PRODRG can create an> *.itp file for that
> > > molecule, so that I can include it in the> generated topology file. But> > > how can I place the molecule in it's original> position? Or even better,> > > how can I convert the original ("full") .pdb
> file for gromacs?> >> > Where's the problem? pdb2gmx makes a .top file for> your non-special> > system, you #include the .itp file for your> special part. There's> > nothing about atomic positions yet have a look
> at a .top file. Now> > grompp takes the .top and some file with atomic> positions and makes a> > .tpr file. Same general procedure as normal.> >> > Mark> > ___
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[gmx-users] special molecule
As I understand, if there are "special" molecules in a pdb file, pdb2gmx cannot convert it. However, PRODRG can create an *.itp file for that molecule, so that I can include it in the generated topology file. But how can I place the molecule in it's original position? Or even better, how can I convert the original ("full") .pdb file for gromacs?
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Re: [gmx-users] Imaging in PBC simulations
I wrote a program using bioJava, that recenters the protein in every frame... that does the job quite nicely, but there maybe other options.On 4/24/06, Martin LEPSIK <[EMAIL PROTECTED]> wrote:Dear GROMACS users, I would like to ask you maybe a trivial question: What is the best wayto image a protein with a ligand insidea triclinic water box?I run an MD in GMX-3.3 with nstcomm=1, "comm_grps" and "comm_mode" not set. I watch the movie in VMD,loading first a starting gro and than the trr. The problem is that theprotein creeps out of the box (the same happenswhen using ngmx).I have tried various variants of post-processing using trjconv -fit (translation) -pbc (inbox, whole) -center (tric),groups for fitting: protein or system. But in any case, the result isthe same.Could you please advice me how to solve this? Whether it is better toinclude some parameter for mdrun or to post-process in a different way?Looking forward to hearing from you.Yours sincerely,Martin LepsikMartin Lepsik, Ph.D.Laboratoire de Dynamique Moléculaire (LDM) Institut de Biologie Structurale41, rue Jules Horowitz38027 Grenoble Cedex 1, Francetel: +33-4-3878-4780e-mail: [EMAIL PROTECTED]___ gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
