[gmx-users] Error by pdb2gmx
Yanmei Song
ysong30 at asu.edu
Wed Apr 29 01:23:44 CEST 2009
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.
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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--
Yanmei Song
Department of Chemical Engineering
ASU
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