[gmx-users] protein topology file fetal error
hi all, i am new to gromacs, when i run my protein file by following the tutorial example mention here( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html) I AM GETTING THE FOLLOWING ERROR FOR MY PROTEIN PDB FILE.. * Fatal error: Atom HA in residue SER 705 was not found in rtp entry SER with 10 atoms while sorting atoms.* PLEASE HELP ME IN REMOVING THIS ERROR WHAT SHOULD I DO TO REMOVE THIS ERROR ? REGARDS kalsoom -- 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! * 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/Support/Mailing_Lists
Re: [gmx-users] dna-drug simulations
On 1/26/13 4:18 AM, amna khan wrote: hi, all , i want to simulate dna with ligand/drug i am getting error in generating he topology for dna . We can't help you unless you show us what the error is and provide (at the very least) your exact pdb2gmx command. I'm unable to do using the pdb2gmx with any of the force fields. Could anyone please tell if I can get any tutorial for the DNA-drug simulation. Exercise Google here. If it exists, you should be able to find it by searching or visiting gromacs.org. or which forcefield should i use ? What does your analysis of the literature suggest would be the best choice? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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! * 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/Support/Mailing_Lists
Re: [gmx-users] protein-SWCNT md simulation
On 1/26/13 4:23 AM, Atila Petrosian wrote: Dear all I want to simulate protein-SWCNT by gromacs. IFf there is a complete tutorial about that, please introduce me. According to the Andrea Minoia's tutorial, there is no problem for MD simulation of the CNT solitude. I have many question about simulation of the protein-SWCNT complex in water. 1) In tutorial, Andrea Minoia mention only to the building CNT+ polymer solvated system and Andrea Minoia did not mention to the force field. If the tutorial you're referring to is http://chembytes.wikidot.com/grocnt, then it is stated that the force field is OPLS-AA. 2) If I use a specific force field for protein to obtain top file (pdb2gmx) and If I use g-x2top to obtain top file for SWCNT, how to do simulation this complex system? You would create a topology that includes a topology for both. Since both pdb2gmx and g_x2top write topologies as .top, you would have to make very simple adjustments to one or both of them to become .itp files to be #included in a master system .top file. See here: http://www.gromacs.org/Documentation/File_Formats/.itp_File Once you have that, you can #include them however you like, CNT .itp within protein .top, or vice versa, or #include both as .itp files within a new .top of your own creation. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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! * 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/Support/Mailing_Lists
Re: [gmx-users] protein topology file fetal error
On 1/26/13 4:41 AM, az kalsom wrote: hi all, i am new to gromacs, when i run my protein file by following the tutorial example mention here( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html) I AM GETTING THE FOLLOWING ERROR FOR MY PROTEIN PDB FILE.. * Fatal error: Atom HA in residue SER 705 was not found in rtp entry SER with 10 atoms while sorting atoms.* PLEASE HELP ME IN REMOVING THIS ERROR WHAT SHOULD I DO TO REMOVE THIS ERROR ? http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry You haven't said exactly what you're dealing with, but if you're trying to use a united-atom force field as in my tutorial, these force fields do not have explicit nonpolar hydrogen atoms. Adding -ignh to pdb2gmx is probably the solution. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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! * 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/Support/Mailing_Lists
[gmx-users] make_ndx error
Hello: I am using make_ndx to make a index file in Gromacs 4.6, make_ndx -f input.pdb but it said: Copied index group 1 'Protein' Copied index group 25 'Water_and_ions' One of your groups is not ascending Group is empty thank you very much best Albert -- 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! * 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/Support/Mailing_Lists
Re: [gmx-users] make_ndx error
On 1/26/13 12:25 PM, Albert wrote: Hello: I am using make_ndx to make a index file in Gromacs 4.6, make_ndx -f input.pdb but it said: Copied index group 1 'Protein' Copied index group 25 'Water_and_ions' One of your groups is not ascending Group is empty What exactly did you enter at the make_ndx prompt? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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! * 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/Support/Mailing_Lists
Re: [gmx-users] make_ndx error
On 01/26/2013 06:53 PM, Justin Lemkul wrote: What exactly did you enter at the make_ndx prompt? -Justin 1|25 protein, water and ions -- 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! * 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/Support/Mailing_Lists
[gmx-users] probems using drude oscillator with ions SWM4-NDP model
Dear gmx users, When I using the drude oscillator model in gromacs, using the SWM4-NDP forcefield with ions in it. I have this kind of problem. Which will cause the calculation failed. Can you give me some advice. = step 11868: EM did not converge in 200 iterations, RMS force 0.023 step 11869: EM did not converge in 200 iterations, RMS force 18.636 step 11870: EM did not converge in 200 iterations, RMS force 66.602 step 11871: EM did not converge in 200 iterations, RMS force 144.795 step 11872: EM did not converge in 200 iterations, RMS force 248.523 step 11873: EM did not converge in 200 iterations, RMS force 365.245 step 11874: EM did not converge in 200 iterations, RMS force 495.880 step 11875: EM did not converge in 200 iterations, RMS force 645.000 step 11876: EM did not converge in 200 iterations, RMS force 815.454 step 11877: EM did not converge in 200 iterations, RMS force 1005.874 step 11878: EM did not converge in 200 iterations, RMS force 1195.862 step 11879: EM did not converge in 200 iterations, RMS force 1369.763 step 11880: EM did not converge in 200 iterations, RMS force 1517.957 step 11881: EM did not converge in 200 iterations, RMS force 1591.082 step 11882: EM did not converge in 200 iterations, RMS force 1581.652 -- Yi Yao Graduate Student Chemistry Department Caudill 006 University of North Carolina at Chapel Hill Email: yaoy...@gmail.com wywyzforever -- 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! * 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/Support/Mailing_Lists
Re: [gmx-users] make_ndx error
On 1/26/13 1:30 PM, Albert wrote: On 01/26/2013 06:53 PM, Justin Lemkul wrote: What exactly did you enter at the make_ndx prompt? -Justin 1|25 protein, water and ions What types of ions do you have? I can reproduce this problem for a protein with ions bound to it, which are numbered discontinuously with water and ions in solution. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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! * 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/Support/Mailing_Lists
Re: [gmx-users] make_ndx error
On 01/26/2013 07:41 PM, Justin Lemkul wrote: What types of ions do you have? I can reproduce this problem for a protein with ions bound to it, which are numbered discontinuously with water and ions in solution. -Justin thank you for kind reply. I only have Na+ and Cl-. best Albert -- 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! * 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/Support/Mailing_Lists
Re: [gmx-users] make_ndx error
On 1/26/13 1:49 PM, Albert wrote: On 01/26/2013 07:41 PM, Justin Lemkul wrote: What types of ions do you have? I can reproduce this problem for a protein with ions bound to it, which are numbered discontinuously with water and ions in solution. -Justin thank you for kind reply. I only have Na+ and Cl-. Can you please post the following: 1. The groups printed in the make_ndx prompt 2. The output of gmxcheck on an index file created from your coordinate file (created simply by typing 'q' at the prompt, i.e. not creating any special groups) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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! * 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/Support/Mailing_Lists
Re: [gmx-users] make_ndx error
On 01/26/2013 07:51 PM, Justin Lemkul wrote: Can you please post the following: 1. The groups printed in the make_ndx prompt 2. The output of gmxcheck on an index file created from your coordinate file (created simply by typing 'q' at the prompt, i.e. not creating any special groups) -Justin make_ndx -f sys.pdb 0 System : 59870 atoms 1 Protein : 4746 atoms 2 Protein-H : 2329 atoms 3 C-alpha : 292 atoms 4 Backbone: 877 atoms 5 MainChain : 1170 atoms 6 MainChain+Cb: 1453 atoms 7 MainChain+H : 1455 atoms 8 SideChain : 3291 atoms 9 SideChain-H : 1159 atoms 10 Prot-Masses : 4746 atoms 11 non-Protein : 55124 atoms 12 Other : 18766 atoms 13 NMA : 6 atoms 14 POPC: 18760 atoms 15 CL :39 atoms 16 NA :34 atoms 17 Ion :73 atoms 18 NMA : 6 atoms 19 POPC: 18760 atoms 20 CL :39 atoms 21 NA :34 atoms 22 Water : 36285 atoms 23 SOL : 36285 atoms 24 non-Water : 23585 atoms 25 Water_and_ions : 36358 atoms gmxcheck_mpi -f md.xtc -n index.ndx Item#frames Timestep (ps) Step 1260.1 Time 1260.1 Lambda 0 Coords 1260.1 Velocities 0 Forces 0 Box1260.1 Contents of index file index.ndx -- Nr. Group #Entries FirstLast 0 System 59870 1 59870 1 Protein 4746 14752 2 Protein-H 2329 12332 3 C-alpha 292 82323 4 Backbone 877 22324 5 MainChain 1170 22325 6 MainChain+Cb1453 22326 7 MainChain+H 1455 24751 8 SideChain 3291 14752 9 SideChain-H 1159 12332 10 Prot-Masses 4746 14752 11 non-Protein551244745 59870 12 Other 187664745 23512 13 NMA647454750 14 POPC 187604753 23512 15 CL39 23513 23585 16 NA34 23518 23551 17 Ion 73 23513 23585 18 NMA647454750 19 POPC 187604753 23512 20 CL39 23513 23585 21 NA34 23518 23551 22 Water 36285 23586 59870 23 SOL36285 23586 59870 24 non-Water 23585 1 23585 25 Water_and_ions 36358 23586 23585 -- 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! * 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/Support/Mailing_Lists
Re: [gmx-users] make_ndx error
On 1/26/13 1:57 PM, Albert wrote: On 01/26/2013 07:51 PM, Justin Lemkul wrote: Can you please post the following: 1. The groups printed in the make_ndx prompt 2. The output of gmxcheck on an index file created from your coordinate file (created simply by typing 'q' at the prompt, i.e. not creating any special groups) -Justin make_ndx -f sys.pdb 0 System : 59870 atoms 1 Protein : 4746 atoms 2 Protein-H : 2329 atoms 3 C-alpha : 292 atoms 4 Backbone: 877 atoms 5 MainChain : 1170 atoms 6 MainChain+Cb: 1453 atoms 7 MainChain+H : 1455 atoms 8 SideChain : 3291 atoms 9 SideChain-H : 1159 atoms 10 Prot-Masses : 4746 atoms 11 non-Protein : 55124 atoms 12 Other : 18766 atoms 13 NMA : 6 atoms 14 POPC: 18760 atoms 15 CL :39 atoms 16 NA :34 atoms 17 Ion :73 atoms 18 NMA : 6 atoms 19 POPC: 18760 atoms 20 CL :39 atoms 21 NA :34 atoms 22 Water : 36285 atoms 23 SOL : 36285 atoms 24 non-Water : 23585 atoms 25 Water_and_ions : 36358 atoms gmxcheck_mpi -f md.xtc -n index.ndx Note that -f is not necessary to produce the needed information, just -n. Item#frames Timestep (ps) Step 1260.1 Time 1260.1 Lambda 0 Coords 1260.1 Velocities 0 Forces 0 Box1260.1 Contents of index file index.ndx -- Nr. Group #Entries FirstLast 0 System 59870 1 59870 1 Protein 4746 14752 2 Protein-H 2329 12332 Something is screwy here - note that gmxcheck finds that the index file has all of the protein heavy atoms first, then all of its hydrogens. Is that correct? It's certainly not normal for any structure processed by pdb2gmx. Besides the point, I suppose. 3 C-alpha 292 82323 4 Backbone 877 22324 5 MainChain 1170 22325 6 MainChain+Cb1453 22326 7 MainChain+H 1455 24751 8 SideChain 3291 14752 9 SideChain-H 1159 12332 10 Prot-Masses 4746 14752 11 non-Protein551244745 59870 12 Other 187664745 23512 13 NMA647454750 14 POPC 187604753 23512 15 CL39 23513 23585 16 NA34 23518 23551 17 Ion 73 23513 23585 18 NMA647454750 19 POPC 187604753 23512 20 CL39 23513 23585 21 NA34 23518 23551 22 Water 36285 23586 59870 23 SOL36285 23586 59870 24 non-Water 23585 1 23585 25 Water_and_ions 36358 23586 23585 Here's the issue. You've got a Water_and_ions group that has over 36k atoms, but it starts by counting backwards! 23586 to 23585 is a size of -1. When you inspect the index file in a text editor, what's in this group? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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! * 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/Support/Mailing_Lists
Re: [gmx-users] error about pbc
Thank Tsjerk so much !
But after being minimized 5 steps and equilibrated 90 ns, there are
some bonds in the system that rotate more than 30 degrees.
I applied tips for blew up system as you advised. But the system does not
achieve balance.
Should i carry out more many steps for minimization ? or minimize many
times ? to get more equilibrated system.
Regards,
KT
On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar wrote:
> Hi KT,
>
> This is caused by another problem. Your system blew up. Check messages
> before this one, and check the log for LINCS warnings.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen >wrote:
>
> > Dear All,
> >
> > My MD simulation has an error
> >
> > Warning: Only triclinic boxes with the first vector parallel to the
> x-axis
> > and the second vector in the xy-plane are supported.
> > Box (3x3):
> > Box[0]={ nan, nan, nan}
> > Box[1]={ nan, nan, nan}
> > Box[2]={ nan, nan, nan}
> > Can not fix pbc.
> >
> > I searched on Gromacs-errors web, but i did not see this error.
> > How can i fix it ?
> >
> > Thanks and regards,
> > KT
> > --
> > 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!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
> --
> gmx-users mailing listgmx-users@gromacs.org
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--
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Re: [gmx-users] error about pbc
On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:
Thank Tsjerk so much !
But after being minimized 5 steps and equilibrated 90 ns, there are
some bonds in the system that rotate more than 30 degrees.
I applied tips for blew up system as you advised. But the system does not
achieve balance.
Should i carry out more many steps for minimization ? or minimize many
times ? to get more equilibrated system.
I would say that 5 steps of minimization is far more than is normally
necessary. What Fmax do you achieve at the end of EM? What is in the system?
What is in your .mdp file? Systems can randomly crash if the model physics
breaks due to incorrect .mdp settings or an unstable topology.
-Justin
On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar wrote:
Hi KT,
This is caused by another problem. Your system blew up. Check messages
before this one, and check the log for LINCS warnings.
Cheers,
Tsjerk
On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen
wrote:
Dear All,
My MD simulation has an error
Warning: Only triclinic boxes with the first vector parallel to the
x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
I searched on Gromacs-errors web, but i did not see this error.
How can i fix it ?
Thanks and regards,
KT
--
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
--
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--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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