[gmx-users] Error by pdb2gmx
Justin A. Lemkul
jalemkul at vt.edu
Fri May 1 02:04:04 CEST 2009
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
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>>>>>>
>>>>>
>>>>> --
>>>>> 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
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>>>>>
>>>> _______________________________________________
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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
>>
>> ========================================
>> _______________________________________________
>> 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!
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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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