[gmx-users] Error by pdb2gmx
Dallas B. Warren
Dallas.Warren at pharm.monash.edu.au
Wed Apr 29 01:03:49 CEST 2009
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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