[gmx-users] grompp: no such moleculetype

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 14 19:22:50 CEST 2009 


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 and are potentially having to hack at.  Read the input, 
determine the appropriate settings and why those you're using may not work.

-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!
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>> or send it to gmx-users-request at gromacs.org.
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>>
>>

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

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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