VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Oct 22 2013 - 10:23:45 CDT

From a quick glance, your force constants look reasonable. Especially for a ring structure, there are many ways to map the potential energy onto specific bonds and angles, so I wouldn't expect to get the same numbers every time.

On Oct 22, 2013, at 7:59 AM, AnkiReddy katha wrote:

> dear Gumbart
>
> Thank you very much for your suggestion, after making those changes, Gaussian (RevC.01) job produced output successfully
>
> I computed the bonded parameters and copied here. There is a difference in the force constants between this calculation and the one in the tutorial (mov files). However equilibrium bond lengths and angles are almost same.
>
> Probably i need to look into optimization of parameters again.
>
> I used Geom.weight 2.0 and Energy weight 1.0 as suggested in your recent JCP paper.
>
> I am not sure how sensitive the parameters will be on the above weights
>
> thank you
> best regards
> Anki
>
> BONDS
> !V(bond) = Kb(b - b0)**2
> !
> !Kb: kcal/mole/A**2
> !b0: A
> !
> !atom type Kb b0
> !
> CG3C52 CG3C52 195.902 1.549
> CG3C52 HGA2 349.074 1.094
> CG3C52 NG3C51 236.790 1.467
> NG3C51 HGP1 435.911 1.024
>
> ANGLES
> !
> !V(angle) = Ktheta(Theta - Theta0)**2
> !
> !V(Urey-Bradley) = Kub(S - S0)**2
> !
> !Ktheta: kcal/mole/rad**2
> !Theta0: degrees
> !Kub: kcal/mole/A**2 (Urey-Bradley)
> !S0: A
> !
> !atom types Ktheta Theta0 Kub S0
> !
> !
> CG3C52 CG3C52 HGA2 49.077 111.205
> CG3C52 CG3C52 CG3C52 134.086 104.836
> CG3C52 CG3C52 NG3C51 117.555 108.982
> CG3C52 NG3C51 HGP1 51.469 108.385
> CG3C52 NG3C51 CG3C52 227.104 102.450
> NG3C51 CG3C52 HGA2 63.435 108.515
> HGA2 CG3C52 HGA2 28.613 107.433
>
>
>
> On Fri, Oct 18, 2013 at 11:58 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> 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
>>
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