[gmx-users] editing .rtp files

[Justin A. Lemkul]

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>
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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