[gmx-users] Error by pdb2gmx
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 29 01:28:44 CEST 2009
Yanmei Song wrote:
> Dear Dallas:
>
> Thanks for your response. It consists of many repeating units. Do you
> mean I can write the rtp entry for one repeating unit and give it a
> residue name. After that I need to insert this into the force field
> rtp file, right? How can I do that? It seems I can not change the rtp
> file. Thanks.
You will need an entry for the repeat units and the terminal/capping groups.
You can make a local copy of the .rtp file and edit it in your working
directory; pdb2gmx will then read this copy when processing your structure.
-Justin
>
> On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren
> <Dallas.Warren at pharm.monash.edu.au> wrote:
>> If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein.
>>
>> 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: Wednesday, 29 April 2009 8:59 AM
>>> To: jalemkul at vt.edu; Discussion list for GROMACS users
>>> Subject: Re: [gmx-users] Error by pdb2gmx
>>>
>>> Dear Justin:
>>>
>>> Do you have any suggestions on how I can get the itp and gro file for
>>> a very long polymer molecules (for example 500 united-atoms), which
>>> only consists of Si, O and C atom. I can use PRODRG to generate a
>>> short chain. But PRODRG has limitation of atom numbers in a molecule,
>>> probably less than 300. So any ideas for building up a long chain
>>> based on the short chain? By the way, I already have the force field
>>> parameters.
>>>
>>> Thanks a lot!
>>>
>>> On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul
>>> <jalemkul at vt.edu> wrote:
>>>>
>>>> Yanmei Song wrote:
>>>>> Dear All users:
>>>>>
>>>>> I was trying to set up a long chain polymer system. I got the
>>>>> following PDB file from WebLab. How can I make changes to
>>> the file in
>>>>> order to make it as a GROMACS input pdb file. Then I can
>>> use pdb2gmx
>>>>> to get the gro, itp and top file.
>>>>>
>>>>> When I perform the pdb2gmx command, I got the error message:
>>>>>
>>>>> Residue 'MOL' not found in residue topology database
>>>>>
>>>> You can't expect pdb2gmx to be magic. A simple search of
>>> the list archives
>>>> and wiki will turn up the following:
>>>>
>>>>
>>> http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not
>> _found_in_residue_topology_database
>>>> -Justin
>>>>
>>>>> Thank you in advance!
>>>>>
>>>>> REMARK Created: Tue Apr 28 15:02:20 US Mountain
>>> Standard Time 2009
>>>>> ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00
>>>>> ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00
>>>>> ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00
>>>>> ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00
>>>>> ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00
>>>>> ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00
>>>>> ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00
>>>>> ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00
>>>>> ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00
>>>>> ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00
>>>>> ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00
>>>>> ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00
>>>>> ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00
>>>>> ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00
>>>>> ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00
>>>>> ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00
>>>>> ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00
>>>>> ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00
>>>>> ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00
>>>>> ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00
>>>>> ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00
>>>>> ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00
>>>>> ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00
>>>>> ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00
>>>>> ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00
>>>>> ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00
>>>>> ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00
>>>>> ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00
>>>>> ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00
>>>>> ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00
>>>>> ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00
>>>>> ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00
>>>>> ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00
>>>>> ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00
>>>>> ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00
>>>>> ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00
>>>>> ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00
>>>>> ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00
>>>>> ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00
>>>>> ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00
>>>>> ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00
>>>>> ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00
>>>>> ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00
>>>>> ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00
>>>>> ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00
>>>>> TER
>>>>>
>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> 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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