[gmx-users] Error by pdb2gmx
Yanmei Song
ysong30 at asu.edu
Thu Apr 30 20:06:50 CEST 2009
Hi, Justin:
Thank you so much for your nice help. I will work on that according to
your suggestions.
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
>>>>>
>>>>> ========================================
>>>>> _______________________________________________
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>>>>
>>>> before posting!
>>>>>
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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
>
> ========================================
> _______________________________________________
> 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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>
--
Yanmei Song
Department of Chemical Engineering
ASU
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