Re: [gmx-users] Thanks to Giovanna! Now, exploding system . . .

Hi! On 8/23/06, Marc Charendoff <[EMAIL PROTECTED]> wrote: With Giovanna's help I was able to complete a grompprun on my system. I did, however get a warning: WARNING 1 [file "topol.top", line 12]:Bad box in file Complex.GROGenerated a cubic box   20.000 x1.445 x1.830   are you sure this me

Re: [gmx-users] periodic boundary condition

yes, they are sufficient. if I remember well, the flag -pbc does the opposite job, it removes periodic boundary conditions. anyway, remember to include in your mdp file the parameters for the treatment of periodic bonudary conditions!   regards,   Maria  On 8/21/06, [EMAIL PROTECTED] <[EMAIL PROTE

Re: [gmx-users] Topology Manipulation question

Hi! you usually get that type of output when the order in which the molecule atoms are written in the topology file (in the itp in your case) does not correspond to the order in the gro file; it might just be that you call the itp corresponding to the second molecule written in the gro file before

Re: [gmx-users] Freezing part of the molecules!!!

Hi!just make an index file (make_ndx) custom-defining the groups which you need to freeze, in your case the C-alpha of residues 18-42. Remember that, when you define new groups, you should delete the corresponding atoms from the group that contains all the rest of the protein atoms, if not you'll g

Re: [gmx-users] errors on restart

Hi Gianluca,the same thing happens to me sometimes too, it seems as if the edr file update is somehow delayed in relation to the other output files, though written with the user defined periodicity. I usually restart from the previous frame. Sorry I can't help more! Greetings,Maria GiovannaOn 5/18/

Re: [gmx-users] atomtype

Hi!I'm sorry, I realize I didn't mention in my first reply that you should download the new version of ffgmx modified for describing lipids to be used with the popc.itp topology file, you can find it at this link: http://www.gromacs.org/topologies/force_fields.php"Invalid order for directive atomty

Re: [gmx-users] popc

Ooops!I mean, I'm using popc.itp, of course!bye,MGOn 5/2/06, MGiò <[EMAIL PROTECTED]> wrote: Hi!I'm using the popc.top which I have downloaded from this website http://moose.bio.ucalgary.ca/index.php?page=Downloadsand the forcefield I'm using is ffgmx, gromacs forcefiel

Re: [gmx-users] popc

Hi!I'm using the popc.top which I have downloaded from this websitehttp://moose.bio.ucalgary.ca/index.php?page=Downloadsand the forcefield I'm using is ffgmx, gromacs forcefield. Cheers,MGOn 5/2/06, mahbubeh zarrabi <[EMAIL PROTECTED]> wrote: hiI try to use make_hole program to make a hole in POPC

[gmx-users] 256 DPPC bilayer

Hi all!I'm desperately looking for a big DPPC bilayer, more than 200 DPPCs. I've read on the mailing list that a 256 lipid bilayer by Lindhal exists, where may I find it? Is it freely downloadable?Thanks for any help, MG ___ gmx-users mailing listgmx-

Re: [gmx-users] grompp error

Hi,are you sure that the DNA_A and DNA_B groups of atoms are correctly defined in the index.ndx file?Actually, it seems that grompp couldn't find them defined because they aren't default groups, so you have to generate a proper user-defined index.ndx file using make_ndx.hope it helps,MGOn 4/4/06,

Re: [gmx-users] error in pdb2gmx step

ny suggestions. Is there any other way in GROMACS to handle proteins with metal ions in it? Thank You, Annie Albin. On 3/31/06, MGiò <[EMAIL PROTECTED] > wrote: Hi!it seems that pdb2gmx has detected an interruption in your chain A numbering, are you sure that there are none? or else are you s

Re: [gmx-users] error in pdb2gmx step

Hi!it seems that pdb2gmx has detected an interruption in your chain A numbering, are you sure that there are none? or else are you sure that you're not using the same chain id for more than one chain? for example for two different monomers? hope it helps,MGOn 3/31/06, Annie Albin < [EMAIL PROTECTED

Re: [gmx-users] Why my protein always falls out of the water box?

Hi you!it may not be as bad as it looks like. Usually the one happening to your protein is only a visualization problem, if an atom of your protein crosses the periodic simulation box, it might appear as if the whole molecule jumps out of the box, because the coordinates of one of its periodic imag

Re: [gmx-users] Not enough ref_t and tau_t values!

Hi Miguel!the same thing happened to me just yesterday. My problem was that, for some reasons not worth to tell, some atoms were missing from one of my groups. I made a new index.ndx file and no errors were reported anymore. So my piece of advice is check your index file. I hope it helps, greeting

Re: [gmx-users] Re: g_hbond

Well,this was my command line:g_hbond -f ../../traj_c.trr -s ../../topol.tpr -g -num -dist -ang -hbn and this was my screen output No option -daReading file ../../topol.tpr, VERSION 3.2.1 (single precision)Specify 2 groups to analyze:Opening library file /usr/local/share/gromacs/top/aminoacids.dat