[gmx-users] Re: gmx-users Digest, Vol 95, Issue 175
Song Ke
song.ke at univie.ac.at
Wed Mar 28 10:16:44 CEST 2012
On Wed, March 28, 2012 00:53, gmx-users-request at gromacs.org wrote:
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> Today's Topics:
>
> 1. Re: WHAM question (lloyd riggs)
> 2. Re: WHAM2 (lloyd riggs)
> 3. Re: amber99sb_virtual site lipids dopc MCH3_N constraint
> types (Mark Abraham)
> 4. Re: dssp error (Mark Abraham)
> 5. Re: Vi plugin for Gromacs files (Szil?rd P?ll)
> 6. Re: Re: How to add dihedral information from the GAFF
> topology (bipin singh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 27 Mar 2012 16:45:55 +0200
> From: "lloyd riggs" <lloyd.riggs at gmx.ch>
> Subject: [gmx-users] Re: WHAM question
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <20120327144555.30940 at gmx.net>
> Content-Type: text/plain; charset="utf-8"
>
> Quick question to anyone,
>
> can you extract energies and forces with g_traj and g_energy and feed them
> to WHAM for molecule by molecule or atom by atom PMF determination. If
> so, how do I get WHAM to read the extracted enrgies as they are written
> out. I did read something about a .pdo file if you have wierdness, that
> it could be used from the past?
>
> Explanation: WHAM works fine for my system, and gives nice curves and
> expected values, however when I try and do this for say a particular amino
> acid by hand the values expected vary. I most likely am just screwing the
> sums (ive been using every term including rest) or theres a difference
> between WHAM and my means of doing the free energy change? I want to stay
> uniform.
>
> Any help or suggestions appriciated
>
> Sincerely
>
> Stephan Watkins
>
>
> --
> NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone!
> Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 27 Mar 2012 16:56:25 +0200
> From: "lloyd riggs" <lloyd.riggs at gmx.ch>
> Subject: [gmx-users] Re: WHAM2
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <20120327145625.83250 at gmx.net>
> Content-Type: text/plain; charset="utf-8"
>
>
> Another WHAM question,
>
> If I use the pullx (position) Vs the pullf(force) i get differ4ent graphs
> but the same overall delG (or PMF).
>
> in the positional one it is a juttery line then at the break point (when
> the protein finally lets go enough) it jumps up to almost its maximum.
> When I use the Force, its a nice smooth graph as from the tutorials? I
> could in reference to the last e-mail use a positional pullx for each
> amino acid, but then this gives a table (which is all I really need) but
> still varies (1-2 kCal/mol for some adding up in the end to alot say 10-15
> kCal/mol or >10% STDDEV)
>
> Stephan
> --
> NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone!
> Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a
>
>
> ------------------------------
>
There is no constraints for the virtual site (CH3)3-N bond in amber
ffbonded.itp in gromacs . And it is important in capped proteins and
lipids virtual site.
Song
> Message: 3
> Date: Wed, 28 Mar 2012 03:20:36 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] amber99sb_virtual site lipids dopc MCH3_N
> constraint types
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F71E8D4.9090201 at anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> On 27/03/2012 11:54 PM, Song Ke wrote:
>> Dear All,
>>
>> I have a question about create and simulate dopc lipid virtual sites. I
>> noticed in ffbonded.itp
>>
>> [ constrainttypes ]
>> ; this section is implemented manually from bond& angle values
>>
>> ; constraints for rigid CH3 groups
>> MCH3 CT 2 0.166426
>> MCH3 S 2 0.193875
>> MCH3 MCH3 2 0.092163
>> ; constraints for rigid NH3 groups
>> MNH3 CT 2 0.158254
>> MNH3 MNH3 2 0.080229
>>
>> ; angle-derived constraints for OH and SH groups in proteins
>> ; The constraint A-C is calculated from the angle A-B-C and bonds A-B,
>> B-C.
>> C HO 2 0.195074
>> CA HO 2 0.195074
>> CT HO 2 0.194132
>> CT HS 2 0.235935
>>
>>
>> However, there is no MCH3 N constraint types, how can I get this value?
>>
>> Meanwhile, Is there a website or scripts to generate the dopc virtual
>> sites bonded itp instead of do it manually?
>
> What's unsatisfactory about pdb2gmx -vsite?
>
> Mark
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 28 Mar 2012 03:21:48 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] dssp error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F71E91C.2050103 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 27/03/2012 8:50 PM, Albert wrote:
>> hello:
>> I am trying to run do_dssp by command:
>>
>> do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm
>>
>> but it said:
>>
>> Select a group: 1
>> Selected 1: 'Protein'
>> There are 35 residues in your selected group
>> trn version: GMX_trn_file (single precision)
>> Reading frame 400 time 400.000
>> Back Off! I just backed up ddbXn2WY to ./#ddbXn2WY.1#
>>
>> -------------------------------------------------------
>> Program do_dssp, VERSION 4.5.5
>> Source code file: do_dssp.c, line: 572
>>
>> Fatal error:
>> Failed to execute command: /usr/local/bin/dssp -na ddbXn2WY ddeWknkk >
>> /dev/null 2> /dev/null
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>
> Sounds like you haven't followed the instructions in do_dssp -h
> carefully enough.
>
> Mark
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 27 Mar 2012 21:43:00 +0200
> From: Szil?rd P?ll <szilard.pall at cbr.su.se>
> Subject: Re: [gmx-users] Vi plugin for Gromacs files
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CANnYEw5z0O=iTy-LbiksXqqvWjC6cd3nD+UP0GFLQQ0xyELD0A at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Hubert,
>
>> With a coworker, we recently developed a plugin Vi to manipulate easily
>> Gromacs files.
>> It enables syntax highlighting for Gromacs files. For the moment, it
>> works
>> with mdp, gro, top/itp and ndx files.
>> It contains also macros to comment/uncomment easily selections of a
>> file.
>
> That's pretty cool, thanks for sharing it!
>
>> Further informations and download can be found in this GitHub
>> repository:
>> https://github.com/HubLot/vim-gromacs
>> Any feedback will be appreciated.
>
> I'll get back with feedback when I'll have used it a bit.
>
>> I hope this is the right place to post it.
>
> Yes, it is, but I'll forward your mail to the devel list just in case
> if some devs have missed it.
>
> We should also consider putting a link on the Gromacs page to your github
> page!
>
> Cheers,
> --
> Szilárd
>
>
>> Best Regards,
>>
>> --
>> Hubert SANTUZ
>> DSIMB Team
>> UMR-S 665, INSERM-Paris Diderot, INTS
>> 6 rue Alexandre Cabanel 75015 Paris, France
>> phone : +33 1 44 49 31 53
>>
>> --
>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 28 Mar 2012 04:22:58 +0530
> From: bipin singh <bipinelmat at gmail.com>
> Subject: Re: [gmx-users] Re: How to add dihedral information from the
> GAFF topology
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <CAKb2Z-FPadFSQ5U1T4=giPmY7RmSw-=005bMDuDWAiPOfu19iA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thanks for your suggestions.
>
> Now I am getting the following error during grompp
>
> Warning: atom name 1 in topol.top and box_prot_oct_sol.gro does not
> match (C1 - N)
> Warning: atom name 5 in topol.top and box_prot_oct_sol.gro does not
> match (C2 - CA)
> Warning: atom name 6 in topol.top and box_prot_oct_sol.gro does not
> match (H4 - HA)
> Warning: atom name 7 in topol.top and box_prot_oct_sol.gro does not
> match (H5 - CB)
> Warning: atom name 8 in topol.top and box_prot_oct_sol.gro does not
> match (C3 - HB1)
> Warning: atom name 9 in topol.top and box_prot_oct_sol.gro does not
> match (H6 - HB2)
> Warning: atom name 10 in topol.top and box_prot_oct_sol.gro does not
> match (H7 - OG)
> Warning: atom name 11 in topol.top and box_prot_oct_sol.gro does not
> match (C4 - HG)
> Warning: atom name 12 in topol.top and box_prot_oct_sol.gro does not
> match (H8 - C)
> Warning: atom name 13 in topol.top and box_prot_oct_sol.gro does not
> match (H9 - O)
> Warning: atom name 14 in topol.top and box_prot_oct_sol.gro does not
> match (C5 - N)
> Warning: atom name 15 in topol.top and box_prot_oct_sol.gro does not
> match (H10 - H)
> Warning: atom name 16 in topol.top and box_prot_oct_sol.gro does not
> match (H11 - CA)
> Warning: atom name 17 in topol.top and box_prot_oct_sol.gro does not
> match (C6 - HA)
> Warning: atom name 18 in topol.top and box_prot_oct_sol.gro does not
> match (H12 - CB)
> Warning: atom name 19 in topol.top and box_prot_oct_sol.gro does not
> match (H13 - HB1)
> Warning: atom name 20 in topol.top and box_prot_oct_sol.gro does not
> match (C7 - HB2)
> Warning: atom name 21 in topol.top and box_prot_oct_sol.gro does not
> match (H14 - CG)
> Warning: atom name 22 in topol.top and box_prot_oct_sol.gro does not
> match (H15 - HG)
> Warning: atom name 23 in topol.top and box_prot_oct_sol.gro does not
> match (C8 - CD1)
> (more than 20 non-matching atom names)
>
> WARNING 1 [file topol.top, line 55]:
> 28782 non-matching atom names
> atom names from topol.top will be used
> atom names from box_prot_oct_sol.gro will be ignored
>
> The order of atoms in coordinate file and order of [molecules]
> directive are same.
> I have checked on the gromacs forum and also the documentation but not
> able to rectify the problem.
>
>
>
> This is how I included the octane topology in .top file
> #########################################
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
> #include "oct.itp"
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Ion_chain_A2.itp"
>
> ; Include water topology
> #include "amber99sb-ildn.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "amber99sb-ildn.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Ion_chain_A2 1
> SOL 565
> 1-octanol 1
> SOL 8422
> ####################################
>
> Please provide suggestions.
>
> On Tue, Mar 27, 2012 at 17:59, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> bipin singh wrote:
>>>
>>> Thanks for your inputs.
>>> I have followed your suggestion and included the .itp for the octane
>>> molecule (containing atomtype definition for new atoms) in the
>>> topology file(.top) of the whole system (prot+oct+water). but during
>>> grompp it produce error and results in termination due to non matching
>>> numbers (27 atoms of octane molecule) between coordinate file and
>>> topology file.
>>>
>>>
>>>
>>> WARNING 1 [file 111-87-5.top, line 15]:
>>> Overriding atomtype h1
>>>
>>>
>>> WARNING 2 [file 111-87-5.top, line 17]:
>>> Overriding atomtype c3
>>>
>>>
>>> WARNING 3 [file 111-87-5.top, line 19]:
>>> Overriding atomtype ho
>>>
>>
>> It appears that you have somehow duplicated atom types and they are
>> overriding each other.
>>
>>
>>> Generated 4656 of the 4656 non-bonded parameter combinations
>>> Generating 1-4 interactions: fudge = 0.5
>>> Generated 4656 of the 4656 1-4 parameter combinations
>>> Excluding 3 bonded neighbours molecule type '1-octanol'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>>> Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
>>> Excluding 3 bonded neighbours molecule type '1-octanol'
>>> Excluding 2 bonded neighbours molecule type 'SOL'
>>> Excluding 2 bonded neighbours molecule type 'SOL'
>>>
>>> NOTE 1 [file topol.top, line 55]:
>>> System has non-zero total charge: -9.999989e-01
>>>
>>> Program grompp, VERSION 4.5.3
>>> Source code file: grompp.c, line: 523
>>>
>>> Fatal error:
>>> number of coordinates in coordinate file (box_oct_sol.gro, 54297)
>>> does not match topology (topol.top, 54324)
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>>
>>
>> Did you follow the link? Surely you would have found:
>>
>> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>>
>> -Justin
>>
>>
>>> ######################################################################3
>>> this is how I included the itp for the octane molecule in .top file
>>>
>>> ; Include forcefield parameters
>>> #include "amber99sb-ildn.ff/forcefield.itp"
>>> #include "octane.itp"
>>>
>>> ; Include chain topologies
>>> #include "topol_Protein_chain_A.itp"
>>> #include "topol_Ion_chain_A2.itp"
>>>
>>> ; Include water topology
>>> #include "amber99sb-ildn.ff/tip3p.itp"
>>>
>>> #ifdef POSRES_WATER
>>> ; Position restraint for each water oxygen
>>> [ position_restraints ]
>>> ; i funct fcx fcy fcz
>>> 1 1 1000 1000 1000
>>> #endif
>>>
>>> ; Include topology for ions
>>> #include "amber99sb-ildn.ff/ions.itp"
>>>
>>> [ system ]
>>> ; Name
>>> Protein in water
>>>
>>> [ molecules ]
>>> ; Compound #mols
>>> Protein_chain_A 1
>>> Ion_chain_A2 1
>>> 1-octanol 1
>>> SOL 565
>>> SOL 8495
>>> #########################################################################
>>>
>>> -------------------------------------------------------
>>>
>>> Please provide your comments.
>>>
>>> On Tue, Mar 27, 2012 at 03:20, Justin A. Lemkul <jalemkul at vt.edu>
>>> wrote:
>>>>
>>>>
>>>> bipin singh wrote:
>>>>>
>>>>> Thanks for your reply.
>>>>>
>>>>> Yes, you are right that these topologies are self supporting and
>>>>> there
>>>>> is no need to to call any other information. I followed your
>>>>> suggestions and able to generate a biphasic system of water/octane
>>>>> containing a protein molecule. But, when I tried grompp on this
>>>>> biphasic system (containing octane+water+protein), it results in
>>>>> error
>>>>> even if I include the topologies in forcefield.itp file.
>>>>>
>>>>> The error was
>>>>>
>>>>> Fatal error:
>>>>> Atomtype hc not found
>>>>> For more information and tips for troubleshooting, please check the
>>>>> GROMACS
>>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>>
>>>> If you introduce a new atomtype in your topology somewhere (presumably
>>>> in
>>>> one of the GAFF topologies), then you have to declare them in an
>>>> [atomtypes]
>>>> directive in the appropriate place in the .top file. These types are
>>>> case
>>>> sensitive as well. For dealing with GAFF-type topologies, assuming
>>>> you
>>>> can
>>>> #include them within whatever AMBER force field you've chosen (up to
>>>> you
>>>> to
>>>> prove), you can do something like:
>>>>
>>>> #include "amberXX.ff/forcefield.itp"
>>>>
>>>> #include "ligand.itp"
>>>>
>>>> [ moleculetype ]
>>>> ;name nrexcl
>>>> Protein 3
>>>>
>>>> (etc)
>>>>
>>>> The inclusion of the ligand topology (at this specific location) will
>>>> add
>>>> the new [atomtypes] at the appropriate level of precedence, before any
>>>> [moleculetypes] are declared.
>>>>
>>>>
>>>> -Justin
>>>>
>>>>> On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul <jalemkul at vt.edu>
>>>>> wrote:
>>>>>>
>>>>>>
>>>>>> bipin singh wrote:
>>>>>>>
>>>>>>> Thanks for your reply.
>>>>>>> But as far as I understood, in order to use these GAFF topology
>>>>>>> (for
>>>>>>> e.g. to perform simulation using these topologies) with Gromacs we
>>>>>>> have to incorporate the information from these topologies to the
>>>>>>> existing Amber forcefields in Gromacs or Is there anyway
>>>>>>> (Possibility
>>>>>>> of using Standalone GAFF parameters in Gromacs) to do it without
>>>>>>> performing this task.
>>>>>>>
>>>>>> As David said, the topologies stand on their own. You do not need
>>>>>> to
>>>>>> call
>>>>>> any further information from anywhere. The .top that you downloaded
>>>>>> begins
>>>>>> with a [defaults] directive, declares atom types, and proceeds
>>>>>> through
>>>>>> the
>>>>>> rest of the topology with explicit parameters.
>>>>>>
>>>>>>
>>>>>>> As you said these topologies are self supporting and we do not need
>>>>>>> to
>>>>>>> change ffbonded.itp, but during grompp I got the following error,
>>>>>>> may
>>>>>>> be because I have not added the dihedral information.
>>>>>>>
>>>>>>> ERROR [file oct.top]:
>>>>>>> No default Proper Dih. types
>>>>>>>
>>>>>>> Please provide your suggestions.
>>>>>>>
>>>>>> I certainly don't see how this could have happened. All the
>>>>>> dihedral
>>>>>> parameters are listed explicitly. The fatal error should have
>>>>>> printed
>>>>>> a
>>>>>> line number in the .top that is problematic, so start by
>>>>>> investigating
>>>>>> there. If you have modified the topology in any way, then undo the
>>>>>> changes
>>>>>> and try again.
>>>>>>
>>>>>> I did not have any trouble using this .top in an unmodified form, so
>>>>>> I
>>>>>> suspect you've altered it in some way that has broken it.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>>> On Mon, Mar 26, 2012 at 17:29, David van der Spoel
>>>>>>> <spoel at xray.bmc.uu.se>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> On 2012-03-26 13:55, bipin singh wrote:
>>>>>>>>>
>>>>>>>>> Hello all,
>>>>>>>>>
>>>>>>>>> I am using the GAFF topology provided for octan-1-ol at Gromacs
>>>>>>>>> liquid
>>>>>>>>> database
>>>>>>>>> (http://virtualchemistry.org/molecules/111-87-5/index.php).
>>>>>>>>> I
>>>>>>>>> have incorporated all the parameters
>>>>>>>>> for atoms, bonds and non-bonded interaction type in the
>>>>>>>>> forcefield
>>>>>>>>> (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top),
>>>>>>>>> but
>>>>>>>>> I
>>>>>>>>> am not sure how to add the dihedraltypes information in
>>>>>>>>> ffbonded.itp
>>>>>>>>> from the GAFF topology as to add this information I need the
>>>>>>>>> phase
>>>>>>>>> and
>>>>>>>>> kd for each dihedral. Is this information is available in the
>>>>>>>>> GAFF
>>>>>>>>> topology provided in the Gromacs database ?
>>>>>>>>>
>>>>>>>>>
>>>>>>>> This topology is self supporting and you do not need anything else
>>>>>>>> in
>>>>>>>> ffbonded.itp.
>>>>>>>>
>>>>>>>> You should be careful merging such parameters with an existing
>>>>>>>> force
>>>>>>>> field,
>>>>>>>> because strictly speaking these are different force fields.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> --
>>>>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>>>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>>>>>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>>>>>>>> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>>>>>>>> --
>>>>>>>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
>>>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> --
>>>>>> ========================================
>>>>>>
>>>>>> Justin A. Lemkul
>>>>>> Ph.D. Candidate
>>>>>> ICTAS Doctoral Scholar
>>>>>> MILES-IGERT Trainee
>>>>>> 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 list gmx-users at 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-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>>
>>>>>
>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> 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 list gmx-users at 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-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> 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 list gmx-users at 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> -----------------------
> Regards,
> Bipin Singh
>
>
> ------------------------------
>
> --
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> End of gmx-users Digest, Vol 95, Issue 175
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