[gmx-users] editing .rtp files

[Jacob Harvey]

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.

Jacob Harvey

-- 
--
Jacob Harvey

Graduate Student

University of Massachusetts Amherst

j.harv8 at gmail.com
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