[gmx-users] Error by pdb2gmx
Dallas B. Warren
Dallas.Warren at pharm.monash.edu.au
Wed Apr 29 01:38:15 CEST 2009
That is correct. Fact you can't edit the .rtp file is based on your local computer system permissions. Normally, best idea is to make your own changes to a local copy, and use that.
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 9:24 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Error by pdb2gmx
>
> 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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