[gmx-users] Error by pdb2gmx
Yanmei Song
ysong30 at asu.edu
Fri May 1 02:11:08 CEST 2009
That means both the rtp and pdb files work in your GROMACS-4.0.4. For
the issue of" PDME residue has a net +0.3 charge" , I should change
the charge to 0 for Si in PDME, which I have ignored. I will update
the software and see if it works. Thanks so much for your help!
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
>>>>>>
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>>>>>>>
>>>>>>> or send it to gmx-users-request at gromacs.org.
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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
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>>>>>>
>>>>> _______________________________________________
>>>>> gmx-users mailing list gmx-users at gromacs.org
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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
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>>> 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!
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>
--
Yanmei Song
Department of Chemical Engineering
ASU
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