[gmx-users] Error by pdb2gmx

Yanmei Song ysong30 at asu.edu
Tue May 5 01:47:02 CEST 2009


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
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>>> 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.
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>



-- 
Yanmei Song
Department of Chemical Engineering
ASU



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