[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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> 
> 
>     -- 
>     ========================================
> 
>     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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