[gmx-users] grompp: no such moleculetype

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 14 20:22:24 CEST 2009 


Francesco Pietra wrote:
> On Wed, Oct 14, 2009 at 7:22 PM, Justin A. Lemkul <jalemkul at vt.edu> 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
>>> lowest stage - the CG tutorial for ubiquitin which is provided on the
>>> MARTINI web page. I encountered the same problem as with my protein.
>>>
>>> I started from files provided in
>>> /output.exercises/protein/protein_data/ubiquitin, i.e.:
>>>
>>> martini_v2.1.itp
>>> cg.gro
>>> cg.itp
>>> cg.top
>>> protein-in-vacuum.mdp
>>>
>>> I commented out all W in cg.top.
>>>
>>> At the command
>>>
>>> $ grompp -np 4 -f protein-in-vacuum.mdp -c cg.gro -p cg.top -o cg.tpr
>>>
>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
>>> checking input for internal consistency...
>>> WARNING 1 [file protein-in-vacuum.mdp, line unknown]:
>>>  For energy conservation with switch/shift potentials, rlist should be 0.1
>>>  to 0.3 nm larger than rcoulomb/rvdw.
>>> calling /lib/cpp...
>>> processing topology...
>>> Generated 0 of the 465 non-bonded parameter combinations
>>> Excluding 1 bonded neighbours for Protein 1
>>> processing coordinates...
>>> Warning: atom names in cg.top and cg.gro don't match (BCQd - BN0)
>>> Warning: atom names in cg.top and cg.gro don't match (SCC5 - SC1)
>>> Warning: atom names in cg.top and cg.gro don't match (BENda - BN0)
>>> Warning: atom names in cg.top and cg.gro don't match (SEP4 - SC1)
>>> Warning: atom names in cg.top and cg.gro don't match (BENda - BN0)
>>> Warning: atom names in cg.top and cg.gro don't match (SEAC1 - SC1)
>>> Warning: atom names in cg.top and cg.gro don't match (BENda - BN0)
>>> Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC1)
>>> Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC2)
>>> Warning: atom names in cg.top and cg.gro don't match (SESC4 - SC3)
>>> Warning: atom names in cg.top and cg.gro don't match (BENda - BN0)
>>> Warning: atom names in cg.top and cg.gro don't match (SEAC2 - SC1)
>>> Warning: atom names in cg.top and cg.gro don't match (BENda - BN0)
>>> Warning: atom names in cg.top and cg.gro don't match (SEC3 - SC1)
>>> Warning: atom names in cg.top and cg.gro don't match (SEQd - SC2)
>>> Warning: atom names in cg.top and cg.gro don't match (BENda - BN0)
>>> Warning: atom names in cg.top and cg.gro don't match (SEP1 - SC1)
>>> Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0)
>>> Warning: atom names in cg.top and cg.gro don't match (STAC1 - SC1)
>>> Warning: atom names in cg.top and cg.gro don't match (BTNda - BN0)
>>> (more than 20 non-matching atom names)
>>> WARNING 2 [file "cg.top", line 22]:
>>>  163 non-matching atom names
>>>  atom names from cg.top will be used
>>>  atom names from cg.gro will be ignored
>>>
>>> double-checking input for internal consistency...
>>> renumbering atomtypes...
>>> converting bonded parameters...
>>> #      BONDS:   160
>>> #  G96ANGLES:   161
>>> #      PDIHS:   9
>>> #      IDIHS:   4
>>> #     CONSTR:   30
>>> Walking down the molecule graph to make shake-blocks
>>> initialising group options...
>>> processing index file...
>>> Analysing residue names:
>>> Opening library file /usr/share/gromacs/top/aminoacids.dat
>>> There are:     0      OTHER residues
>>> There are:    76    PROTEIN residues
>>> There are:     0        DNA residues
>>> Analysing Protein...
>>>
>>> -------------------------------------------------------
>>> Program grompp, VERSION 3.3.3
>>> Source code file: ../../../../src/kernel/readir.c, line: 798
>>>
>>> Fatal error:
>>> Group Non-Protein not found in indexfile.
>>> Maybe you have non-default goups in your mdp file, while not using the
>>> '-n' option of grompp.
>>> In that case use the '-n' option.
>>> =================
>>>
>>>> From the name "protein-in-vacuum.mdp" I assume that there is no "HOH"
>> You know what happens when you assume...
>>
>>> 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.
>>>
>> Read the .mdp file you're using.  There are two very clear appearances of
>> the Non-Protein term (energygrps and tc-grps).  Don't simply trust an .mdp
>> file you found somewhere
> 
> was not found "somewhere". It is the file provided by the author of
> that tutorial right for that tutorial (everything was taken from the
> solution provided to the example).
> 

Indeed, it may work in certain cases, but my general advice is simply this: if 
you didn't make it yourself with manual in hand, you have to still comb through 
it to make sure it addresses your system.  If you have only protein, and 
Non-Protein is defined somewhere, then the .mdp file does not suit your needs. 
I have also seen many instances of files that "work" in tutorials (topologies, 
scripts, .mdp files) wind up not working when I look into them.  This is not to 
say that any particular individual has posted anything incorrectly, but always 
check your input for yourself!

> 
>> and are potentially having to hack at.  Read the
>> input, determine the appropriate settings and why those you're using may not
>> work.
> 
> I'll look at. But I fear that by commenting out what alludes to
> non-protein (if this is what I should do; if not, please explain what
> I should do), it will not work. It was so with "my protein".
> 

If your system has only protein, then a suitable setting for both the energygrps 
and tc-grps would be either "Protein" or "System", since they are essentially 
equivalent in this case.  If you have only protein, then nothing should be 
non-protein, right?  The combination of "Protein Non-Protein" in these settings 
is designed for a simulation of protein in solvent, and perhaps ions, to prevent 
unsuspecting users from coupling ions separately to a thermostat (which usually 
leads to a crash).

> At any event, for a person like me coming from AMBER, it is surprising
> that there is no "minimum" input that works with every standard
> protein.
> 

I think that this could be dangerous.  Different force fields were parameterized 
for different cutoffs, vdW and electrostatics methods, etc, and so it may be 
desirable to adhere rigorously to the appropriate settings, given the diversity 
of force fields available in GROMACS (GROMOS, OPLS, AMBER, CHARMM soon, CG 
models).  Many parameters can be left at the default, but others would certainly 
require a bit of user input to be assured of their validity :)

-Justin

> Thanks
> francesco
>> -Justin
>>
>>> thanks
>>>
>>> francesco pietra
>>>
>>>
>>>
>>>
>>> On Mon, Oct 5, 2009 at 11:14 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>> Francesco Pietra wrote:
>>>>
>>>>>> Look at the .mdp file.  You will find Non-Protein somewhere.
>>>>> The .mdp I used is not from a tutorial; it is the general purpose - or
>>>>> standard - mdp provided by Martini. It doe not contain the word
>>>>> "protein"
>>>>>
>>>>> The "protein-in-vacuum.mdp from the ubiquitin CG tutoria does contain
>>>>> both "Protein" and "Non-Protein" words. deleting "Non-Protein", the
>>>>> error from running grompp is:
>>>>>
>>>>> Fatal error:
>>>>> Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values
>>>>>
>>>> This comes up because you've defined one group now for T-coupling and
>>>> assigned coupling constants and temperatures for two.  Haphazard changes
>>>> to
>>>> .mdp files will certainly generate these errors.  Deleting until the
>>>> problem
>>>> goes away never works - it only creates more problems :)
>>>>
>>>> Please see the manual for proper use of tc-grps, etc.
>>>>
>>>>>>> I'll settle the matter until I can generate ideas, or be less tired to
>>>>>>> check again for the presence of that mysterious non-protein. The real
>>>>>>> protein contains chloride ion ligands. I have cleared from them before
>>>>>>> starting with CG and anyway no trace of cl CL Cl.
>>>>>>>
>>>>>> So that has nothing to do with it.
>>>>>>
>>>>>>> Hope to be able to come again here with a solution of this affair.
>>>>>>>
>>>>>> The best advice - don't blindly use some .mdp file you find because it
>>>>>> works
>>>>>> for a tutorial.  Read it, read the manual, and make changes based on
>>>>>> what
>>>>>> you actually have in your system.
>>>>> I fully agree. Using "protein-in-vacuum.mdp", although attractive
>>>>> because of "vacuum", was a bold adventure. But the standard mdp I used
>>>>> before is declared to be standard, and my protein is standard. As I
>>>>> said, I'll work hard to come out but before I'll take a few days
>>>>> wandering with my Brittany on the Alps. The Tetraonidae will refresh
>>>>> my mind.
>>>>>
>>>> What is "standard" for one user is not necessarily "standard" for
>>>> another.
>>>>  You must almost always make changes to suit your particular system, as a
>>>> general rule.
>>>>
>>>>> Thanks for all you did for me (for us)
>>>>>
>>>> You're welcome.  Hopefully everything works out.
>>>>
>>>> -Justin
>>>>
>>>>> francesco
>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>> thanks
>>>>>>> francesco
>>>>>>> PS: the protein CG file contains TER lines separating the subunits,
>>>>>>> but the CG .gro file has no TER.
>>>>>>>
>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>>> ;
>>>>>>>>> ; mod21 | MARTINI 2.1
>>>>>>>>> ;
>>>>>>>>>
>>>>>>>>> ; Include force field poarameters containing all particle
>>>>>>>>> definitions,
>>>>>>>>> ; the interaction matrix, plus the topology for water.
>>>>>>>>>
>>>>>>>>> #include "martini_v2.1.itp"
>>>>>>>>>
>>>>>>>>> ; Then include the file(s) containing the topologies of other
>>>>>>>>> ; molecules present in your system.
>>>>>>>>>
>>>>>>>>> ; #include "martini_v2.0_lipids.itp"
>>>>>>>>> ; #include "martini_v2.0_salt.itp"
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> #include "mod21.itp"
>>>>>>>>>
>>>>>>>>> ; Define a name for your system
>>>>>>>>>
>>>>>>>>> [ system ]
>>>>>>>>> mod21
>>>>>>>>>
>>>>>>>>> ; Define the composition of your system
>>>>>>>>> ; The molecule names should correspond to those defined in the itp
>>>>>>>>> file(s).
>>>>>>>>>
>>>>>>>>> [ molecules ]
>>>>>>>>> Protein 1
>>>>>>>>> ; DPPC 128
>>>>>>>>> ; W 2000
>>>>>>>>> ; NA+ 20
>>>>>>>>> ; CL- 20
>>>>>>>>>
>>>>>>>>> It seems that commenting out ";" is placed correctly.
>>>>>>>>>
>>>>>>>>> I am sincerely sorry to bother you again.
>>>>>>>>>
>>>>>>>>> francesco
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>> With command
>>>>>>>>>>>
>>>>>>>>>>> $ grompp -np 4 -f mod21.cg.mdp -c mod21.cg.box.gro -p mod21.cg.top
>>>>>>>>>>> -n
>>>>>>>>>>> -o mod21.cg.tpr
>>>>>>>>>>>
>>>>>>>>>>> NOTE:
>>>>>>>>>>>  System has non-zero total charge: -5.000000e+01
>>>>>>>>>>>
>>>>>>>>>>> processing coordinates...
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (BCQd - BN0)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SCAC1 - SC1)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (BCP5 - BN0)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SCP1 - SC1)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (BSP5 - BN0)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SSAC1 - SC1)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (BCP5 - BN0)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SCC3 - SC1)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SCQd - SC2)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (BCP5 - BN0)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SCN0 - SC1)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SCQd - SC2)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (BHN0 - BN0)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (BHNd - BN0)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SHAC1 - SC1)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (BHNd - BN0)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SHSC4 - SC2)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SHSP1 - SC1)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SHSC4 - SC3)
>>>>>>>>>>> Warning: atom names in mod21.cg.top and mod21.cg.box.gro don't
>>>>>>>>>>> match
>>>>>>>>>>> (SHSC4 - SC4)
>>>>>>>>>>> (more than 20 non-matching atom names)
>>>>>>>>>>> WARNING 2 [file "mod21.cg.top", line 28]:
>>>>>>>>>>>  2875 non-matching atom names
>>>>>>>>>>>  atom names from mod21.cg.top will be used
>>>>>>>>>>>  atom names from mod21.cg.box.gro will be ignored
>>>>>>>>>>>
>>>>>>>>>>> double-checking input for internal consistency...
>>>>>>>>>>> renumbering atomtypes...
>>>>>>>>>>> converting bonded parameters...
>>>>>>>>>>> #      BONDS:   2724
>>>>>>>>>>> #  G96ANGLES:   2860
>>>>>>>>>>> #      PDIHS:   328
>>>>>>>>>>> #      IDIHS:   187
>>>>>>>>>>> #     CONSTR:   745
>>>>>>>>>>> Walking down the molecule graph to make shake-blocks
>>>>>>>>>>> initialising group options...
>>>>>>>>>>> processing index file...
>>>>>>>>>>>
>>>>>>>>>>> -------------------------------------------------------
>>>>>>>>>>> Program grompp, 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?
>>>>>>>>>>>
>>>>>>>>>> Non-matching names occur because MARTINI doesn't assign them
>>>>>>>>>> correctly
>>>>>>>>>> in
>>>>>>>>>> the initial system setup.  Using the .top names is fine.
>>>>>>>>>>
>>>>>>>>>> The I/O error comes from the fact that you have passed the -n flag
>>>>>>>>>> to
>>>>>>>>>> grompp
>>>>>>>>>> without having index.ndx in the working directory.  Note that
>>>>>>>>>> having
>>>>>>>>>> an
>>>>>>>>>> index file doesn't necessarily solve your problem; the warning is
>>>>>>>>>> printed
>>>>>>>>>> in
>>>>>>>>>> case you have non-default groups for, e.g., T-coupling or
>>>>>>>>>> energygrps.
>>>>>>>>>>  If
>>>>>>>>>> you have a "moleculetype not found," then you haven't #included the
>>>>>>>>>> .itp
>>>>>>>>>> file and an index file won't save you.
>>>>>>>>>>
>>>>>>>>>> -Justin
>>>>>>>>>>
>>>>>>>>>>> Thanks for help
>>>>>>>>>>> francesco
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Mon, Oct 5, 2009 at 12:33 PM, Justin A. Lemkul
>>>>>>>>>>> <jalemkul at vt.edu>
>>>>>>>>>>> wrote:
>>>>>>>>>>>> Francesco Pietra wrote:
>>>>>>>>>>>>> Hi:
>>>>>>>>>>>>>
>>>>>>>>>>>>> As I found it difficult to manage solvation - the way I would
>>>>>>>>>>>>> like
>>>>>>>>>>>>> -
>>>>>>>>>>>>> with a pore protein (a trimer) partly immersed into a bilayer, I
>>>>>>>>>>>>> started with the protein alone in vacuum, in order to try to fix
>>>>>>>>>>>>> the
>>>>>>>>>>>>> problems step-by-step. Unfortunately, I can't fix simple
>>>>>>>>>>>>> problems
>>>>>>>>>>>>> with
>>>>>>>>>>>>> grompp.
>>>>>>>>>>>>>
>>>>>>>>>>>>> 1) Generated mod21.itp from mod21.pdb
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2) Generated mod21.cg.pdb with awk script)
>>>>>>>>>>>>>
>>>>>>>>>>>>> 3) editconf -f mod21.cg.pdb -o mod21.cg.gro
>>>>>>>>>>>>>
>>>>>>>>>>>>> 4) genbox -cp mod21.cg.gro -box 10 17 10 -o mod21.cg.box.gro
>>>>>>>>>>>>>
>>>>>>>>>>>>> 5) grompp -np 4 -f mod21.cg.box.mdp  -c mod21.cg.box.gro -p
>>>>>>>>>>>>> mod21.cg.box.top -warnmax 10
>>>>>>>>>>>>>
>>>>>>>>>>>>>  Error: no such moleculetype Protein.
>>>>>>>>>>>>>
>>>>>>>>>>>>> .............................
>>>>>>>>>>>>> .mdp is merely a renamed martini_v2.0.example.mdp, taking care
>>>>>>>>>>>>> that
>>>>>>>>>>>>> "cpp  = /usr/bin/cpp".
>>>>>>>>>>>>>
>>>>>>>>>>>>> .top was from editing martini_v2.0.example.top and reads (in
>>>>>>>>>>>>> between
>>>>>>>>>>>>> ===):
>>>>>>>>>>>>> ======
>>>>>>>>>>>>> ;
>>>>>>>>>>>>> ; mod21 | MARTINI 2.1
>>>>>>>>>>>>> ;
>>>>>>>>>>>>>
>>>>>>>>>>>>> ; Include force field parameters containing all particle
>>>>>>>>>>>>> definitions,
>>>>>>>>>>>>> ; the interaction matrix, plus the topology for water.
>>>>>>>>>>>>>
>>>>>>>>>>>>> #include "martini_v2.1.itp"
>>>>>>>>>>>>>
>>>>>>>>>>>>> ; Then include the file(s) containing the topologies of other
>>>>>>>>>>>>> ; molecules present in your system.
>>>>>>>>>>>>>
>>>>>>>>>>>>> ; #include "martini_v2.0_lipids.itp"
>>>>>>>>>>>>> ; #include "martini_v2.0_salt.itp"
>>>>>>>>>>>>>
>>>>>>>>>>>>> #include mod21.itp
>>>>>>>>>>>>>
>>>>>>>>>>>> This #include statement has the wrong syntax.  See any of the
>>>>>>>>>>>> above
>>>>>>>>>>>> for
>>>>>>>>>>>> the
>>>>>>>>>>>> correct way to do it.
>>>>>>>>>>>>
>>>>>>>>>>>> -Justin
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> ========================================
>>>>>>>>>>>>
>>>>>>>>>>>> Justin A. Lemkul
>>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>>> ICTAS Doctoral Scholar
>>>>>>>>>>>> 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/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/mailing_lists/users.php
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> ========================================
>>>>>>>>>>
>>>>>>>>>> Justin A. Lemkul
>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>> ICTAS Doctoral Scholar
>>>>>>>>>> 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/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/mailing_lists/users.php
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>> --
>>>>>>>> ========================================
>>>>>>>>
>>>>>>>> Justin A. Lemkul
>>>>>>>> Ph.D. Candidate
>>>>>>>> ICTAS Doctoral Scholar
>>>>>>>> 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/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/mailing_lists/users.php
>>>>>>>>
>>>>>>>>
>>>>>> --
>>>>>> ========================================
>>>>>>
>>>>>> Justin A. Lemkul
>>>>>> Ph.D. Candidate
>>>>>> ICTAS Doctoral Scholar
>>>>>> 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/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/mailing_lists/users.php
>>>>>>
>>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> 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/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/mailing_lists/users.php
>>>>
>>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> 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/search before posting!
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>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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