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From: AnkiReddy katha (kathaankireddy_at_gmail.com)
Date: Tue Oct 22 2013 - 06:59:59 CDT
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- In reply to: JC Gumbart: "Re: FFTK, pyrrolidine parametrization bonded parameters- issue with Hessian"
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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
>
>
>
- Next message: Mayne, Christopher G: "Re: fftk-charges"
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- In reply to: JC Gumbart: "Re: FFTK, pyrrolidine parametrization bonded parameters- issue with Hessian"
- Next in thread: JC Gumbart: "Re: FFTK, pyrrolidine parametrization bonded parameters- issue with Hessian"
- Reply: JC Gumbart: "Re: FFTK, pyrrolidine parametrization bonded parameters- issue with Hessian"
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