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 <jalem...@vt.edu
<mailto:jalem...@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.ha...@gmail.com <mailto:j.ha...@gmail.com>
<mailto:j.ha...@gmail.com <mailto:j.ha...@gmail.com>>
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========================================
Justin A. Lemkul
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ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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University of Massachusetts Amherst
j.ha...@gmail.com <mailto:j.ha...@gmail.com>
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________________________________________________________________________
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