[gmx-users] Error by pdb2gmx
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 30 19:46:58 CEST 2009
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
>>>>
>>>> ========================================
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>>>
>>>
>>> --
>>> Yanmei Song
>>> Department of Chemical Engineering
>>> ASU
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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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