[gmx-users] editing .rtp files
David van der Spoel
spoel at xray.bmc.uu.se
Sun Apr 5 20:48:31 CEST 2009
Jacob Harvey wrote:
> Thanks for your help Justin. Looks like I am still having issues though.
> Now I get the error:
>
> "Fatal error:
> Residue 'IMD' not found in residue topology database"
>
> I am trying to create a topolgy file using pdb2gmx with the OPLS-AA
> force field and I have added the following entry to the ffoplsaa.rtp
> file. Also I have added IMD to aminoacid.dat but I dont think that is
> necessary for running pdb2gmx. Any ideas where I'm going wrong?
>
Did you increase the number at the top of the aminoacids.dat file?
You may also need to add a record in the .hdb file (unless you have all
hydrogen positions already).
Finally you could try pdb2gmx -debug 1 and check the pdb2gmx.debug file
for more information.
> Jacob
>
> [ IMD ]
>
> [ atoms ]
> NA opls_557 -0.257 1
> CR opls_558 0.275 1
> NB opls_559 -0.563 1
> CV opls_560 0.185 1
> CW opls_561 -0.286 1
> H opls_562 0.306 1
> HA1 opls_563 0.078 1
> HA2 opls_564 0.075 1
> HA3 opls_565 0.187 1
> CT1 opls_139 0.000 1
> CT2 opls_139 0.000 1
> CT3 opls_139 0.000 1
> CT4 opls_139 0.000 1
> HC1 opls_140 0.060 1
> HC2 opls_140 0.060 1
> HC3 opls_140 0.060 1
> HC4 opls_140 0.060 1
> HC5 opls_140 0.060 1
> HC6 opls_140 0.060 1
> HC7 opls_140 0.060 1
> HC8 opls_140 0.060 1
> HC9 opls_140 0.060 1
>
> [ bonds ]
> CT1 HC1
> CT1 HC2
> CT1 HC3
> CT1 CT2
> CT2 HC4
> CT2 HC5
> CT2 CT3
> CT3 HC6
> CT3 HC7
> CT3 CT4
> CT4 HC8
> CT4 HC9
> CT4 CR
> CR NB
> NB CV
> CV HA2
> CV CW
> CW HA3
> CW NA
> NA H
> NA CR
>
> On Sat, Apr 4, 2009 at 7:36 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Jacob Harvey wrote:
>
> Dear All,
>
> I am having issues editing a .rtp file (ffoplsaa.rtp to be
> exact). I want to create a new residue for my system so that I
> can generate a topology file using pdb2gmx. This is the code
> that I have added to the .rtp file:
>
> [ IMD ]
> [ atoms ]
> NA opls_557 -.257 1
> CR opls_558 .275 1
> NB opls_559 -.563 1
> CV opls_560 .185 1
> CW opls_561 -.286 1
> H opls_562 .306 1
> HA1 opls_563 .078 1
> HA2 opls_564 .075 1
> HA3 opls_565 .187 1
> CT1 opls_139 .000 1
> CT2 opls_139 .000 1
> CT3 opls_139 .000 1
> CT4 opls_139 .000 1
> HC1 opls_140 .060 1
> HC2 opls_140 .060 1
> HC3 opls_140 .060 1
> HC4 opls_140 .060 1
> HC5 opls_140 .060 1
> HC6 opls_140 .060 1
> HC7 opls_140 .060 1
> HC8 opls_140 .060 1
> HC9 opls_140 .060 1
>
> [ bonds ]
> CT1 HC1
> CT1 HC2
> CT1 HC3
> CT1 CT2
> CT2 HC4
> CT2 HC5
> CT2 CT3
> CT3 HC6
> CT3 HC7
> CT3 CT4
> CT4 HC8
> CT4 HC9
> CT4 CR
> CR NB
> NB CV
> CV HA2
> CV CW
> CW HA3
> CW NA
> NA H
> NA CR
>
> And this is my pdb file (at least a portion of it):
>
> ATOM 1 CT1 IMD 1 -4.438 3.334 2.988
> ATOM 2 CT1 IMD 2 0.588 3.313 0.517
> ATOM 3 CT1 IMD 3 5.476 3.310 -2.216
> ATOM 4 HC1 IMD 1 -4.134 2.590 3.731
> ATOM 5 HC2 IMD 1 -5.525 3.438 3.047
> ATOM 6 HC3 IMD 1 -3.996 4.291 3.276
> ATOM 7 HC1 IMD 2 1.480 3.111 1.117
> ATOM 8 HC2 IMD 2 -0.266 3.349 1.200
> ATOM 9 HC3 IMD 2 0.702 4.307 0.076
> ATOM 10 HC1 IMD 3 6.375 3.525 -1.633
> ATOM 11 HC2 IMD 3 4.648 3.862 -1.761
> ATOM 12 HC3 IMD 3 5.628 3.709 -3.223
> ATOM 13 CT2 IMD 1 -3.996 2.922 1.581
> ATOM 14 HC4 IMD 1 -2.902 2.862 1.545
> ATOM 15 HC5 IMD 1 -4.281 3.703 0.865
> ATOM 16 CT2 IMD 2 0.394 2.242 -0.557
> ATOM 17 HC4 IMD 2 -0.485 2.486 -1.167
> ATOM 18 HC5 IMD 2 1.250 2.252 -1.242
> ATOM 19 CT2 IMD 3 5.188 1.805 -2.247
> ATOM 20 HC4 IMD 3 6.018 1.286 -2.742
> ATOM 21 HC5 IMD 3 4.300 1.615 -2.864
> ATOM 22 CT3 IMD 1 -4.587 1.582 1.127
> ATOM 23 HC6 IMD 1 -5.682 1.638 1.161
>
>
> However when I run the code "pdb2gmx -f filename.pdb" I get the
> following error:
>
> "Fatal error:
> Residue 'MD' not found in residue topology database"
>
> Whats wrong with the way I edited the .rtp file? And why is
> pdb2gmx only recognizing the first two letter of the residue
> (why wouldn't it say "Residue IMD" because thats what I named it
> in the PDB file)? Thanks in advance for the help.
>
>
> It looks like you're off by a space in the format of your .pdb file,
> so pdb2gmx is not seeing the initial "I"; I posted the link to the
> PDB format guide the other day; have another look and see where you
> may have gone wrong.
>
> -Justin
>
> Jacob Harvey
>
> --
> --
> Jacob Harvey
>
> Graduate Student
>
> University of Massachusetts Amherst
>
> j.harv8 at gmail.com <mailto:j.harv8 at gmail.com>
> <mailto:j.harv8 at gmail.com <mailto:j.harv8 at gmail.com>>
>
>
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>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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>
>
>
> --
> --
> Jacob Harvey
>
> Graduate Student
>
> University of Massachusetts Amherst
>
> j.harv8 at gmail.com <mailto:j.harv8 at gmail.com>
>
>
> ------------------------------------------------------------------------
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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