[gmx-users] Error by pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Tue May 5 01:53:53 CEST 2009


Then it seems clear to me that your installation of Gromacs is faulty.  Have you 
tried running the test set (available on the wiki site)?  If you can describe 
your computer system (OS, version, compilers used, configuration options, etc.) 
then perhaps someone on the list can spot a potential pitfall.

-Justin

Yanmei Song wrote:
> Dear Justin:
> 
> Thank you so much for your help earlier. I updated my GROMACS to
> 4.0.4. When I run pdb2gmx using the following two files. I still got
> the similar error message:
> 
> Opening library file ffoplsaa.rtp
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
> WARNING: masses will be determined based on residue and atom names,
>          this can deviate from the real mass of the atom type
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat
> Entries in atommass.dat: 178
> WARNING: vdwradii will be determined based on residue and atom names,
>          this can deviate from the real mass of the atom type
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat
> Entries in vdwradii.dat: 28
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat
> Entries in dgsolv.dat: 7
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat
> Entries in electroneg.dat: 71
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat
> Entries in elements.dat: 218
> Reading pdms2.pdb...
> Read 13 atoms
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat
> 26 out of 26 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
> 
>   chain  #res #atoms
>   1 ' '     3     13
> 
> All occupancies are one
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp
> Atomtype 1
> Reading residue database... (ffoplsaa)
> Opening library file ffoplsaa.rtp
> 
> -------------------------------------------------------
> Program pdb2gmx_d, VERSION 4.0.4
> Source code file: resall.c, line: 279
> 
> Fatal error:
> in .rtp file at line:
> 
> 
> -------------------------------------------------------
> 
> My new residue added to ffoplass.rtp is:
> [ PDM ]
> ; designation arbitrary, C1 and C2 is -CH3
>   [ atoms ]
>     SI1   SI           0.300    1
>      C1   opls_069     0.000    1
>      C2   opls_069     0.000    1
>      O1   opls_108    -0.300    1
> 
>   [ bonds ]
>     SI1   -O1
>     SI1   C1
>     SI1   C2
>     SI1   O1
>      O1   +SI1
> 
> 
> ; Terminal PDMS residue ("beginning" of chain)
> ; designation arbitrary, C1 C2 and C3 is -CH3
> [ PDMB ]
>   [ atoms ]
>     C1    opls_069     0.000    1
>    SI1    SI           0.300    1
>     C2    opls_069     0.000    1
>     C3    opls_069     0.000    1
>     O1    opls_108    -0.300    1
> 
>   [ bonds ]
>     SI1   C1
>     SI1   C2
>     SI1   C3
>     SI1   O1
>      O1   +SI1
> 
> 
> ; Terminal PE residue ("end" of chain)
> ; designation arbitrary, C1 C2 and C3 is -CH3
> 
> [ PDME ]
>   [ atoms ]
>     SI1    SI          0.000    1
>     C1    opls_069     0.000    1
>     C2    opls_069     0.000    1
>     C3    opls_069     0.000    1
> 
>   [ bonds ]
>     SI1   -O1
>     SI1   C1
>     SI1   C2
>     SI1   C3
> 
> PDB file:
> 
> ATOM      1 SI1  PDMB    1       8.995  -3.779  -2.091  1.00  0.00
> ATOM      2  C1  PDMB    1      10.682  -3.453  -2.828  1.00  0.00
> ATOM      3  C2  PDMB    1       8.020  -2.184  -2.039  1.00  0.00
> ATOM      4  O1  PDMB    1       8.142  -4.958  -3.082  1.00  0.00
> ATOM      5  C3  PDMB    1       9.192  -4.446  -0.356  1.00  0.00
> ATOM      6 SI1  PDM     2       6.710  -5.932  -3.395  1.00  0.00
> ATOM      7  O1  PDM     2       6.960  -6.886  -4.852  1.00  0.00
> ATOM      8  C1  PDM     2       6.403  -7.074  -1.946  1.00  0.00
> ATOM      9  C2  PDM     2       5.231  -4.812  -3.628  1.00  0.00
> ATOM     10 SI1  PDME    3       6.370  -8.062  -6.022  1.00  0.00
> ATOM     11  C1  PDME    3       7.679  -8.351  -7.325  1.00  0.00
> ATOM     12  C2  PDME    3       5.990  -9.673  -5.153  1.00  0.00
> ATOM     13  C3  PDME    3       4.816  -7.411  -6.834  1.00  0.00
> TER
> 
> Thanks a lot!
> 
> 
> 
> 
> 
> On Thu, Apr 30, 2009 at 5:04 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> Your system works for me under Gromacs 4.0.4 - the only issue is that your
>> PDME residue has a net +0.3 charge.  Does your Gromacs installation work
>> properly for proven systems like proteins?
>>
>> I would suggest upgrading to version 4.0.4 and trying again.  If that does
>> not work, post to the list a complete description of your hardware and
>> software - OS, version, compilers used, configuration options, etc, and see
>> if anyone can spot a problem.
>>
>> -Justin
>>
>> Yanmei Song wrote:
>>> Sorry to bother so many times.
>>>
>>> I edited the rtp and added the new residue as following, which I think
>>> should be no problem.
>>>
>>> [ PDM ]
>>>
>>>  [ atoms ]
>>>    SI1    SI                 0.300    1
>>>     C1   opls_069     0.000    1
>>>     C2   opls_069     0.000    1
>>>     O1   opls_108    -0.300    1
>>>
>>>  [ bonds ]
>>>    SI1   -O1
>>>    SI1    C1
>>>    SI1    C2
>>>    SI1    O1
>>>    O1   +SI1
>>>
>>>
>>> ; Terminal  PDMS residue ("beginning" of chain)
>>>
>>> [ PDMB ]
>>>  [ atoms ]
>>>    C1    opls_069     0.000    1
>>>   SI1     SI                 0.300    1
>>>    C2    opls_069     0.000    1
>>>    C3    opls_069     0.000    1
>>>    O1    opls_108    -0.300    1
>>>
>>>  [ bonds ]
>>>    SI1   C1
>>>    SI1   C2
>>>    SI1   C3
>>>    SI1   O1
>>>     O1   +SI1
>>>
>>>
>>> ; Terminal PDMS residue ("end" of chain)
>>>
>>>
>>> [ PDME ]
>>>  [ atoms ]
>>>   SI1     SI                 0.300    1
>>>    C1    opls_069     0.000    1
>>>    C2    opls_069     0.000    1
>>>    C3    opls_069     0.000    1
>>>
>>>  [ bonds ]
>>>    SI1   -O1
>>>    SI1   C1
>>>    SI1   C2
>>>    SI1   C3
>>>
>>> Also my pdb is :
>>>
>>> ATOM      1 SI1  PDMB    1       8.995  -3.779  -2.091  1.00  0.00
>>> ATOM      2  C1  PDMB    1      10.682  -3.453  -2.828  1.00  0.00
>>> ATOM      3  C2  PDMB    1       8.020  -2.184  -2.039  1.00  0.00
>>> ATOM      4  O1  PDMB    1       8.142  -4.958  -3.082  1.00  0.00
>>> ATOM      5  C3  PDMB    1       9.192  -4.446  -0.356  1.00  0.00
>>> ATOM      6 SI1  PDM     2       6.710  -5.932  -3.395  1.00  0.00
>>> ATOM      7  O1  PDM     2       6.960  -6.886  -4.852  1.00  0.00
>>> ATOM      8  C1  PDM     2       6.403  -7.074  -1.946  1.00  0.00
>>> ATOM      9  C2  PDM     2       5.231  -4.812  -3.628  1.00  0.00
>>> ATOM     10 SI1  PDME    3       6.370  -8.062  -6.022  1.00  0.00
>>> ATOM     11  C1  PDME    3       7.679  -8.351  -7.325  1.00  0.00
>>> ATOM     12  C2  PDME    3       5.990  -9.673  -5.153  1.00  0.00
>>> ATOM     13  C3  PDME    3       4.816  -7.411  -6.834  1.00  0.00
>>> TER
>>>
>>> after pdb2gmx, I still got the error:
>>>
>>> Opening library file ffoplsaa.rtp
>>> Opening library file
>>> /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
>>> Reading pdms2.pdb...
>>> Read 13 atoms
>>> Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
>>> 26 out of 26 lines of xlateat.dat converted succesfully
>>> Analyzing pdb file
>>> There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
>>>
>>>  chain  #res #atoms
>>>  1 ' '     3     13
>>>
>>> All occupancies are one
>>> Opening library file
>>> /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
>>> Atomtype 817
>>> Reading residue database... (ffoplsaa)
>>> Opening library file ffoplsaa.rtp
>>>
>>> -------------------------------------------------------
>>> Program pdb2gmx, VERSION 3.3.3
>>> Source code file: resall.c, line: 289
>>>
>>> Fatal error:
>>> in .rtp file at line:
>>>
>>>
>>> -------------------------------------------------------
>>>
>>> Anyone knows where I did wrong?
>>>
>>> Thank you so much!
>>> On Thu, Apr 30, 2009 at 10:46 AM, Justin A. Lemkul <jalemkul at vt.edu>
>>> wrote:
>>>> Yanmei Song wrote:
>>>>> Hi, Dallas:
>>>>>
>>>>> I added this to the ffoplsaa.rtp
>>>>>
>>>>> [ PDM ]
>>>>>
>>>>> [ atoms ]
>>>>>     SI       SI                 0.300     1
>>>>>  CH3      opls_069    0.000     1
>>>>>      O       opls_108   -0.300     1
>>>>>
>>>>>  [ bonds ]
>>>>>   SI     O
>>>>>   SI   CH3
>>>>>
>>>>>
>>>>>  [ dihedrals ]
>>>>>  CH3    SI    O      SI     dih_PDM_chi1_C_SI_O_SI
>>>>>     SI     O   SI   CH3     dih_PDM_chi1_SI_O_SI_C
>>>>>      O    SI    O      SI      dih_PDM_chi1_O_SI_O_SI
>>>>>
>>>>> The format is the same with other entries. Do you guys think anything
>>>>> wrong with it?
>>>>>
>>>>> Also what does it mean by the error message:
>>>>>
>>>>> Opening library file ffoplsaa.rtp
>>>>> Opening library file
>>>>> /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
>>>>> Reading pdms10.pdb...
>>>>> Read 45 atoms
>>>>> Opening library file
>>>>> /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
>>>>> 26 out of 26 lines of xlateat.dat converted succesfully
>>>>> Analyzing pdb file
>>>>> There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
>>>>>
>>>>>  chain  #res #atoms
>>>>>  1 'A'     1     45
>>>>>
>>>>> All occupancies are one
>>>>> Opening library file
>>>>> /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
>>>>> Atomtype 817
>>>>> Reading residue database... (ffoplsaa)
>>>>> Opening library file ffoplsaa.rtp
>>>>>
>>>>> -------------------------------------------------------
>>>>> Program pdb2gmx, VERSION 3.3.3
>>>>> Source code file: resall.c, line: 289
>>>>>
>>>>> Fatal error:
>>>>> in .rtp file at line:
>>>>>
>>>>>
>>>>> -------------------------------------------------------
>>>>>
>>>>> what is "Source code file: resall.c, line: 289"  It seems the problem
>>>>> comes from here.
>>>> That is the line of code that is spotting a problem.
>>>>
>>>> I think the issue is that, in your original .pdb file, you have dozens of
>>>> atoms in your polymer chain, all labeled as residue 1.  What your .rtp
>>>> entry
>>>> says is that a single PDM should contain only three atoms.  Since what
>>>> you
>>>> are trying to do is make a building block, you will need to do several
>>>> things:
>>>>
>>>> 1. Re-number your .pdb file so that multiple monomers are apparent.
>>>> 2. Use the + and - characters to indicate connectivity to the next
>>>> residue
>>>> and previous residue, respectively.
>>>> 3. Create separate .rtp entries for terminal groups, as I suggested
>>>> previously, so that termini are handled correctly (since the -n.tdb and
>>>> -c.tdb files cannot be used for non-protein).
>>>>
>>>> See the amino acid entries for examples on how to use + and -
>>>> appropriately,
>>>> or the list archive for examples provided by other users for other
>>>> polymers
>>>> (polyethylene is especially common), for example:
>>>>
>>>> http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html
>>>>
>>>> -Justin
>>>>
>>>>> Thanks a lot!
>>>>>
>>>>>
>>>>> On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren
>>>>> <Dallas.Warren at pharm.monash.edu.au> wrote:
>>>>>> Check consistency with other entries around it, easy way to check to
>>>>>> see
>>>>>> that you have the right format.
>>>>>>
>>>>>> What did you edit the file with?
>>>>>>
>>>>>> Catch ya,
>>>>>>
>>>>>> Dr. Dallas Warren
>>>>>> Department of Pharmaceutical Biology and Pharmacology
>>>>>> Pharmacy and Pharmaceutical Sciences, Monash University
>>>>>> 381 Royal Parade, Parkville VIC 3010
>>>>>> dallas.warren at pharm.monash.edu.au
>>>>>> +61 3 9903 9167
>>>>>> ---------------------------------
>>>>>> When the only tool you own is a hammer, every problem begins to
>>>>>> resemble
>>>>>> a nail.
>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: gmx-users-bounces at gromacs.org
>>>>>>> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
>>>>>>> Sent: Thursday, 30 April 2009 9:07 AM
>>>>>>> To: jalemkul at vt.edu; Discussion list for GROMACS users
>>>>>>> Subject: Re: [gmx-users] Error by pdb2gmx
>>>>>>>
>>>>>>> This is the new entry I added to the rtp file.
>>>>>>>
>>>>>>> [ PDM ]
>>>>>>>
>>>>>>>
>>>>>>>  [ atoms ]
>>>>>>>   SI      SI              0.300     1
>>>>>>>  CH3    opls_069    0.000     1
>>>>>>>    O      opls_108   -0.300     1
>>>>>>>
>>>>>>>
>>>>>>>  [ bonds ]
>>>>>>>   SI     O       0.190    158805.0
>>>>>>>   SI   CH3     0.164    293160.0
>>>>>>>
>>>>>>>
>>>>>>>  [ dihedrals ]
>>>>>>>  CH3    SI    O    SI   3.77    3     0
>>>>>>>   SI     O   SI   CH3   3.77    3     0
>>>>>>>    O    SI    O    SI     3.77    3     0
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
>>>>>>> <jalemkul at vt.edu> wrote:
>>>>>>>> Yanmei Song wrote:
>>>>>>>>
>>>>>>>>> -------------------------------------------------------
>>>>>>>>> Program pdb2gmx, VERSION 3.3.3
>>>>>>>>> Source code file: resall.c, line: 289
>>>>>>>>>
>>>>>>>>> Fatal error:
>>>>>>>>> in .rtp file at line:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> -------------------------------------------------------
>>>>>>>> Well that's not a terribly helpful error message, is it? :)
>>>>>>>>
>>>>>>>> There is probably something wrong with the .rtp entry you
>>>>>>> created.  If you
>>>>>>>> can post that, perhaps someone can spot 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://www.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
>>>>>>>>
>>>>>>> --
>>>>>>> Yanmei Song
>>>>>>> Department of Chemical Engineering
>>>>>>> ASU
>>>>>>> _______________________________________________
>>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>>> http://www.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
>>>>>>>
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>>> http://www.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://www.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://www.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

========================================



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