[gmx-users] grompp: no such moleculetype
Francesco Pietra
francesco.pietra at accademialucchese.it
Wed Oct 14 19:19:55 CEST 2009
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"
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.
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
>
>
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