Re: Create psf file

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Jun 22 2015 - 10:01:23 CDT

Siska,

When using the toppar files generated from the CGenFF Program, make sure that you double check the residue name. In the file you attached, CGenFF has named the residue "Molecu", which I suspected is not the residue name given in the PDB.

Regards,
Christopher Mayne

> Dear NAMD user,
> I want to ask, how to create psf file if we have ligand file and already get the topology and parameter file from cgenff?I tried to use the automatic psf builder in VMD, it is failed. then I tried to make the psf file manually (using the script) and it also failed.Here attached the pdb file of my ligand and also the topology and parameter file that I got from cgenff.
> Anyone can help me please?
> Thank you for your help.
> Regards,Siska
>
> [demime 1.01d removed an attachment of type application/octet-stream]
> * Toppar stream file generated by
> * CHARMM General Force Field (CGenFF) program version 1.0.0
> * For use with CGenFF version 3.0.1
> *
>
> read rtf card append
> * Topologies generated by
> * CHARMM General Force Field (CGenFF) program version 1.0.0
> *
> 36 1
>
> ! "penalty" is the highest penalty score of the associated parameters.
> ! Penalties lower than 10 indicate the analogy is fair; penalties between 10
> ! and 50 mean some basic validation is recommended; penalties higher than
> ! 50 indicate poor analogy and mandate extensive validation/optimization.
>
> RESI Molecu -3.000 ! param penalty= 443.000 ; charge penalty= 203.396
> GROUP ! CHARGE CH_PENALTY
> ATOM C1 CG2R61 -0.204 ! 6.998
> ATOM C2 CG2R61 -0.121 ! 10.387
> ATOM C3 CG2R61 0.193 ! 127.615
> ATOM C4 CG2R61 -0.121 ! 10.387
> ATOM C5 CG2R61 -0.204 ! 6.998
> ATOM C6 CG2R61 -0.398 ! 0.000
> ATOM H1 HGR61 0.210 ! 0.000
> ATOM H2 HGR61 0.115 ! 0.800
> ATOM H3 HGR61 0.115 ! 0.800
> ATOM H4 HGR61 0.210 ! 0.000
> ATOM N1 NG2D1 -0.193 ! 139.702
> ATOM N2 NG2D1 -0.367 ! 203.396
> ATOM C7 CG2R51 0.404 ! 200.906
> ATOM C8 CG2R51 -0.003 ! 94.220
> ATOM C9 CG2R52 0.251 ! 92.569
> ATOM N3 NG2R51 0.206 ! 78.283
> ATOM N4 NG2R50 -0.530 ! 44.563
> ATOM O1 OG311 -0.525 ! 66.108
> ATOM H5 HGP1 0.420 ! 5.130
> ATOM C10 CG2O3 0.552 ! 86.175
> ATOM O2 OG2D2 -0.760 ! 4.985
> ATOM C11 CG2R61 0.104 ! 67.045
> ATOM C12 CG2R61 -0.116 ! 4.624
> ATOM C13 CG2R61 -0.116 ! 4.624
> ATOM C14 CG2R61 -0.205 ! 2.131
> ATOM H6 HGR61 0.115 ! 0.250
> ATOM C15 CG2R61 -0.205 ! 2.131
> ATOM H7 HGR61 0.115 ! 0.250
> ATOM C16 CG2R61 -0.398 ! 0.000
> ATOM H8 HGR61 0.210 ! 0.000
> ATOM H9 HGR61 0.210 ! 0.000
> ATOM S1 SG3O1 1.348 ! 0.000
> ATOM O3 OG2P1 -0.650 ! 0.000
> ATOM O4 OG2P1 -0.650 ! 0.000
> ATOM S2 SG3O1 1.348 ! 0.000
> ATOM O5 OG2P1 -0.650 ! 0.000
> ATOM O6 OG2P1 -0.650 ! 0.000
> ATOM O7 OG2P1 -0.650 ! 0.000
> ATOM O8 OG2D2 -0.760 ! 4.985
> ATOM O9 OG2P1 -0.650 ! 0.000
>
> BOND C1 C2
> BOND C1 C6
> BOND C1 H1
> BOND C2 C3
> BOND C2 H2
> BOND C3 C4
> BOND C3 N1
> BOND C4 C5
> BOND C4 H3
> BOND C5 C6
> BOND C5 H4
> BOND C6 S1
> BOND N1 N2
> BOND N2 C7
> BOND C7 C8
> BOND C7 C9
> BOND C8 N3
> BOND C8 O1
> BOND C9 N4
> BOND C9 C10
> BOND N3 N4
> BOND N3 C11
> BOND O1 H5
> BOND C10 O2
> BOND C10 O8
> BOND C11 C12
> BOND C11 C13
> BOND C12 C14
> BOND C12 H6
> BOND C13 C15
> BOND C13 H7
> BOND C14 C16
> BOND C14 H8
> BOND C15 C16
> BOND C15 H9
> BOND C16 S2
> BOND S1 O3
> BOND S1 O4
> BOND S1 O9
> BOND S2 O5
> BOND S2 O6
> BOND S2 O7
> IMPR C10 O8 O2 C9
>
> END
>
> read param card flex append
> * Parameters generated by analogy by
> * CHARMM General Force Field (CGenFF) program version 1.0.0
> *
>
> ! Penalties lower than 10 indicate the analogy is fair; penalties between 10
> ! and 50 mean some basic validation is recommended; penalties higher than
> ! 50 indicate poor analogy and mandate extensive validation/optimization.
>
> BONDS
> CG2O3 CG2R52 200.00 1.5000 ! Molecu , from CG2O3 CG2R61, penalty= 45
> CG2R51 NG2D1 500.00 1.3100 ! Molecu , from CG2N1 NG2D1, penalty= 175
> CG2R51 OG311 334.30 1.4110 ! Molecu , from CG2R61 OG311, penalty= 45
> CG2R61 NG2D1 305.00 1.4140 ! Molecu , from CG2R61 NG2S1, penalty= 160
> CG2R61 NG2R51 400.00 1.3900 ! Molecu , from CG2R61 NG2S3, penalty= 50
> NG2D1 NG2D1 500.00 1.2760 ! Molecu , from CG2DC1 NG2D1, penalty= 400
>
> ANGLES
> CG2R52 CG2O3 OG2D2 40.00 116.00 50.00 2.35300 ! Molecu , from CG2R61 CG2O3 OG2D2, penalty= 8.5
> CG2R51 CG2R51 NG2D1 60.80 127.50 ! Molecu , from CG2R51 CG2R53 OG2D1, penalty= 64
> CG2R51 CG2R51 OG311 120.00 111.00 ! Molecu , from CG2R51 CG2R51 NG3P2, penalty= 39
> CG2R52 CG2R51 NG2D1 60.80 127.50 ! Molecu , from CG2R51 CG2R53 OG2D1, penalty= 66
> NG2R51 CG2R51 OG311 45.80 124.00 ! Molecu , from CG321 CG2R51 NG2R51, penalty= 45
> CG2O3 CG2R52 CG2R51 45.80 130.00 ! Molecu , from CG2R51 CG2R51 CG321, penalty= 80
> CG2O3 CG2R52 NG2R50 45.80 120.00 ! Molecu , from CG321 CG2R51 NG2R50, penalty= 80
> CG2R61 CG2R61 NG2D1 40.00 120.00 35.00 2.41620 ! Molecu , from CG2R61 CG2R61 NG2S1, penalty= 16
> CG2R61 CG2R61 NG2R51 60.00 121.00 ! Molecu , from CG2R61 CG2R61 NG2S3, penalty= 5
> CG2R51 NG2D1 NG2D1 100.00 115.00 ! Molecu , from CG2D1 NG2D1 NG2S1, penalty= 82
> CG2R61 NG2D1 NG2D1 100.00 115.00 ! Molecu , from CG2D1 NG2D1 NG2S1, penalty= 82
> CG2R51 NG2R51 CG2R61 70.00 127.10 ! Molecu , from CG2R51 NG2R51 CG321, penalty= 71
> CG2R61 NG2R51 NG2R50 70.00 117.90 ! Molecu , from CG321 NG2R51 NG2R50, penalty= 71
> CG2R51 OG311 HGP1 65.00 108.00 ! Molecu , from CG2R61 OG311 HGP1, penalty= 8.5
>
> DIHEDRALS
> OG2D2 CG2O3 CG2R52 CG2R51 3.1000 2 180.00 ! Molecu , from OG2D2 CG2O3 CG2R61 CG2R61, penalty= 93.5
> OG2D2 CG2O3 CG2R52 NG2R50 3.1000 2 180.00 ! Molecu , from OG2D2 CG2O3 CG2R61 CG2R61, penalty= 130
> CG2R52 CG2R51 CG2R51 OG311 0.4100 1 180.00 ! Molecu , from CG2R51 CG2R51 CG2R53 OG3C51, penalty= 59.6
> NG2D1 CG2R51 CG2R51 NG2R51 14.0000 2 180.00 ! Molecu , from NG2R50 CG2R51 CG2R51 NG2R51, penalty= 45
> NG2D1 CG2R51 CG2R51 OG311 3.0000 2 180.00 ! Molecu , from CG321 CG2R51 CG2R51 NG2R50, penalty= 90
> CG2R51 CG2R51 CG2R52 CG2O3 15.0000 2 180.00 ! Molecu , from CG2R51 CG2R51 CG2R51 CG2R51, penalty= 75.5
> NG2D1 CG2R51 CG2R52 CG2O3 3.0000 2 180.00 ! Molecu , from CG321 CG2R51 CG2R51 NG2R50, penalty= 125
> NG2D1 CG2R51 CG2R52 NG2R50 9.5000 2 180.00 ! Molecu , from NG2R50 CG2R52 CG2R52 NG2R50, penalty= 50
> CG2R51 CG2R51 NG2D1 NG2D1 1.2000 2 180.00 ! Molecu , from CG2R61 CG2R61 NG2S1 CG2O1, penalty= 346.5
> CG2R52 CG2R51 NG2D1 NG2D1 1.2000 2 180.00 ! Molecu , from CG2R61 CG2R61 NG2S1 CG2O1, penalty= 346.5
> CG2R51 CG2R51 NG2R51 CG2R61 3.0000 2 180.00 ! Molecu , from CG2R51 CG2R51 NG2RC0 CG2R61, penalty= 40
> OG311 CG2R51 NG2R51 CG2R61 3.0000 2 180.00 ! Molecu , from CG321 CG2R51 NG2R51 CG2R53, penalty= 97
> OG311 CG2R51 NG2R51 NG2R50 3.0000 2 180.00 ! Molecu , from CG321 CG2R51 NG2R51 CG2R53, penalty= 94.5
> CG2R51 CG2R51 OG311 HGP1 0.9900 2 180.00 ! Molecu , from CG2R61 CG2R61 OG311 HGP1, penalty= 93.5
> NG2R51 CG2R51 OG311 HGP1 0.9900 2 180.00 ! Molecu , from CG2R61 CG2R61 OG311 HGP1, penalty= 132
> CG2O3 CG2R52 NG2R50 NG2R51 12.0000 2 180.00 ! Molecu , from CG2R51 CG2R52 NG2R50 NG2R51, penalty= 70.5
> CG2R61 CG2R61 CG2R61 NG2D1 3.1000 2 180.00 ! Molecu , from CG2R61 CG2R61 CG2R61 NG2S1, penalty= 16
> CG2R61 CG2R61 CG2R61 NG2R51 5.0000 2 180.00 ! Molecu , from CG2R61 CG2R61 CG2R61 NG2S3, penalty= 5
> NG2D1 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! Molecu , from NG2S1 CG2R61 CG2R61 HGR61, penalty= 16
> NG2R51 CG2R61 CG2R61 HGR61 2.4000 2 180.00 ! Molecu , from NG2S3 CG2R61 CG2R61 HGR61, penalty= 5
> CG2R61 CG2R61 NG2D1 NG2D1 1.2000 2 180.00 ! Molecu , from CG2R61 CG2R61 NG2S1 CG2O1, penalty= 253
> CG2R61 CG2R61 NG2R51 CG2R51 1.2000 2 180.00 ! Molecu , from CG2R61 CG2R61 NG2S1 CG2O1, penalty= 170
> CG2R61 CG2R61 NG2R51 NG2R50 1.2000 2 180.00 ! Molecu , from CG2R61 CG2R61 NG2S1 CG2O1, penalty= 193
> CG2R51 NG2D1 NG2D1 CG2R61 12.0000 2 180.00 ! Molecu , from CG2R61 CG2DC1 NG2D1 NG2S1, penalty= 443
> CG2R52 NG2R50 NG2R51 CG2R61 8.5000 2 180.00 ! Molecu , from CG2R52 NG2R50 NG2R51 CG2RC0, penalty= 47.5
>
> IMPROPERS
> CG2O3 OG2D2 OG2D2 CG2R52 96.0000 0 0.00 ! Molecu , from CG2O3 OG2D2 OG2D2 CG2R61, penalty= 4.5
>
> END
> RETURN

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