From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Oct 18 2013 - 13:28:42 CDT

Try changing the routing and input format to match this:

# MP2/6-31G* Geom=(ModRedundant,AllCheck) NoSymm IOp(7/33=1) SCF=Tight Freq Guess=Read

B * * K
A * * * K
L * * * K
D * * * * K
B 2 1 A
B 14 1 A
B 30 1 A
...

so instead of specifying the internal coordinates directly, you have Gaussian get them from the checkpoint file.

Let me know if this works for you!
JC

On Oct 17, 2013, at 3:44 AM, AnkiReddy katha wrote:

> dear all
>
> I am trying to use fftk for parametrization of pyrrolidine molecule as per the tutorial (mov files in the web page)
>
> i used "VMD for LINUXAMD64, version 1.9.2a33 (August 19, 2013)".
>
> obtaining partial charges was done successfully
>
> for bonded interactions, i generated a gaussian input for Hessian calculations. However Gaussian (g09) run exits with the error.
>
> final few lines from the output:
>
> The following ModRedundant input section has been read:
> B * * R
> A * * * R
> L * * * * R
> D * * * * R
> Unrecognized coordinate type "O"
> Error termination via Lnk1e in /apps/Gaussian/g09_C.01/g09/l101.exe at Thu Oct 17 14:56:13 2013.
> Job cpu time: 0 days 0 hours 0 minutes 0.8 seconds.
> File lengths (MBytes): RWF= 17 Int= 0 D2E= 0 Chk= 3 Scr= 2
>
> Here i copied gaussian input file as well.
> O****R is there in the input file, i am not sure it is really needed .
> Does anybody has resolved this kind of problem ?
> I am still in the learning stage of Gaussian
>
> thank you
> best regards
> Anki
>
> Gaussian input file (prld-hess.gau):
>
> %chk=prld-hess.chk
> %nproc=4
> %mem=4GB
> # MP2/6-31G* Geom=(AllCheck,ModRedundant) Freq NoSymm IOp(7/33=1) SCF=Tight
>
> B * * R
> A * * * R
> L * * * R
> D * * * * R
> O * * * * R
> B 2 1 1.5458859205245972
> B 5 1 1.5473904609680176
> B 9 1 1.0942554473876953
> B 10 1 1.0945135354995728
> B 3 2 1.4689862728118896
> B 7 2 1.095960259437561
> B 8 2 1.0939182043075562
> B 4 3 1.4694414138793945
> B 6 3 1.022707223892212
> B 5 4 1.5453675985336304
> B 11 4 1.095273494720459
> B 12 4 1.0949742794036865
> B 13 5 1.0947282314300537
> B 14 5 1.09366774559021
> A 3 2 1 106.94517517089844
> A 7 2 1 110.2688980102539
> A 8 2 1 113.6523208618164
> A 4 5 1 103.9924087524414
> A 13 5 1 110.7358627319336
> A 14 5 1 112.60598754882813
> A 5 1 2 104.00730895996094
> A 9 1 2 110.35113525390625
> A 10 1 2 112.04695129394531
> A 4 3 2 102.72390747070313
> A 6 3 2 107.79466247558594
> A 7 2 3 107.58104705810547
> A 8 2 3 110.63500213623047
> A 5 4 3 106.96168518066406
> A 11 4 3 107.59465026855469
> A 12 4 3 110.62216186523438
> A 6 3 4 107.76542663574219
> A 13 5 4 110.3781967163086
> A 14 5 4 112.04817199707031
> A 9 1 5 110.75652313232422
> A 10 1 5 112.58296966552734
> A 11 4 5 110.27906036376953
> A 12 4 5 113.63633728027344
> A 8 2 7 107.61500549316406
> A 10 1 9 107.14501953125
> A 12 4 11 107.60529327392578
> A 14 5 13 107.13017272949219
> D 7 2 1 5 93.2771224975586
> D 8 2 1 5 -145.797607421875
> D 3 2 1 5 -23.410436630249023
> D 7 2 1 9 -147.8998260498047
> D 8 2 1 9 -26.974437713623047
> D 3 2 1 9 95.41273498535156
> D 7 2 1 10 -28.596086502075195
> D 8 2 1 10 92.32929992675781
> D 3 2 1 10 -145.2836456298828
> D 4 5 1 2 -0.017617572098970413
> D 14 5 1 2 -121.53909301757813
> D 13 5 1 2 118.54100799560547
> D 4 5 1 9 -118.56297302246094
> D 14 5 1 9 119.91567993164063
> D 13 5 1 9 -0.004356699530035257
> D 4 5 1 10 121.49931335449219
> D 14 5 1 10 -0.0221601203083992
> D 13 5 1 10 -119.94219207763672
> D 4 3 2 1 38.13874435424805
> D 6 3 2 1 -75.50143432617188
> D 4 3 2 7 -80.31403350830078
> D 6 3 2 7 166.04591369628906
> D 4 3 2 8 162.3939666748047
> D 6 3 2 8 48.753780364990234
> D 11 4 3 2 80.31867218017578
> D 12 4 3 2 -162.40008544921875
> D 5 4 3 2 -38.16173553466797
> D 11 4 3 6 -166.01986694335938
> D 12 4 3 6 -48.738494873046875
> D 5 4 3 6 75.49984741210938
> D 1 5 4 3 23.43535614013672
> D 14 5 4 3 145.32765197753906
> D 13 5 4 3 -95.36844635009766
> D 1 5 4 11 -93.28309631347656
> D 14 5 4 11 28.609201431274414
> D 13 5 4 11 147.91322326660156
> D 1 5 4 12 145.80784606933594
> D 14 5 4 12 -92.29998779296875
> D 13 5 4 12 27.004037857055664
> 1,1 Top
>