[gmx-users] editing .rtp files
Jacob Harvey
j.harv8 at gmail.com
Sun Apr 5 20:11:52 CEST 2009
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?
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> 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>
>>
>>
>> ------------------------------------------------------------------------
>>
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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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--
--
Jacob Harvey
Graduate Student
University of Massachusetts Amherst
j.harv8 at gmail.com
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