3
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As above, I am attempting to generate an IC table for decanoic acid using CHARMM (version 48b1) so I have a minimized geometry. I have attached my build.inp script and the stream file I have written. I am having issues with the alkyl hydrogens bonding to two carbons in a manner similar to the C-C bond. I based my stream file on the all_36_lipid_detergents.str file that comes with CHARMM, removing two carbons from lauric acid to create my decanoic acid stream file.

Does anybody have advice about how to fix my hydrogens? I have attached my build.inp, stream file and the generated pdb along with a vmd generated image of the lipid.

build.inp

* Reads the DCA residue from the stream topology file and writes a pdb consisting
* of a single DCA molecule
*

!topology and parameter files

stream toppar.str

read sequence DECA 1
generate DECA

!read sequence DECN 1
!generate DECN

ic generate
ic param
ic seed 1 C1 1 C2 1 C3 !to generate box CHARMM must know coords of at least three atoms defined by top file
ic build

open write card unit 10 name DCA_build.pdb
write coor pdb  unit 10

top_dca.str

* Topology file for decanoic acid and decanoate
* Stream following reading of
* top_all36_lipid.rtf
* and
* par_all36_lipid.rtf
*

!Based on fatty acids LAU and LAUP added Jan 2016 

read rtf card append
* decanoic acid and decanoate
*
41  1

AUTOGENERATE ANGLE DIHE

RESI DECA        0.00 ! Decanoic Acid (10:0)
GROUP                 !
ATOM H1   HOL    0.44 !
ATOM O1   OHL   -0.61 !      O2  O1--H1
ATOM O2   OBL   -0.55 !       \\ /
ATOM C1   CL     0.75 !        C1
ATOM C2   CTL2  -0.21 !         |
ATOM H2R  HAL2   0.09 !  H2R---C2---H2S
ATOM H2S  HAL2   0.09 !         |       
GROUP                 !
ATOM C3   CTL2  -0.18 !         |
ATOM H3R  HAL2   0.09 !  H3R---C3---H3S
ATOM H3S  HAL2   0.09 !         |
GROUP                 !
ATOM C4   CTL2  -0.18 !         |
ATOM H4R  HAL2   0.09 !  H4R---C4---H4S
ATOM H4S  HAL2   0.09 !         |
GROUP                 !
ATOM C5   CTL2  -0.18 !         |
ATOM H5R  HAL2   0.09 !  H5R---C5---H5S
ATOM H5S  HAL2   0.09 !         |
GROUP                 !
ATOM C6   CTL2  -0.18 !         |
ATOM H6R  HAL2   0.09 !  H6R---C6---H6S
ATOM H6S  HAL2   0.09 !         |
GROUP                 !
ATOM C7   CTL2  -0.18 !         |
ATOM H7R  HAL2   0.09 !  H7R---C7---H7S
ATOM H7S  HAL2   0.09 !         |
GROUP                 !
ATOM C8   CTL2  -0.18 !         |
ATOM H8R  HAL2   0.09 !  H8R---C8---H8S
ATOM H8S  HAL2   0.09 !         |
GROUP                 !
ATOM C9   CTL2  -0.18 !         |
ATOM H9R  HAL2   0.09 !  H9R---C9---H9S
ATOM H9S  HAL2   0.09 !         |
GROUP                 !
ATOM C10  CTL3  -0.27 !         |
ATOM H10S HAL3   0.09 ! H10R---C10--H10S
ATOM H10R HAL3   0.09 !         |
ATOM H10T HAL3   0.09 !        H10T

BOND  O1  H1
BOND  O1  C1
BOND  C1  C2
DOUBLE  C1  O2
BOND  C2  H2R       C2  H2S       C2  C3
BOND  C3  H3R       C3  H3S       C3  C4
BOND  C4  H4R       C4  H4S       C4  C5
BOND  C5  H5R       C5  H5S       C5  C6
BOND  C6  H6R       C6  H6S       C6  C7
BOND  C7  H7R       C7  H7S       C7  C8
BOND  C8  H8R       C8  H8S       C8  C9
BOND  C9  H9R       C9  H9S       C9  C10
BOND  C10 H10R      C10 H10S      C10 H10T

IMPR C1 O1 C2 O2

RESI DECN       -1.00 ! Decanoic acid (10:0), unprotonated
GROUP                 !
ATOM O1   OCL   -0.76 !      O2  O1 (-)
ATOM O2   OCL   -0.76 !       \\ /
ATOM C1   CL     0.62 !        C1
ATOM C2   CTL2  -0.28 !         |
ATOM H2R  HAL2   0.09 !  H2R---C2---H2S
ATOM H2S  HAL2   0.09 !         |       
GROUP                 !
ATOM C3   CTL2  -0.18 !         |
ATOM H3R  HAL2   0.09 !  H3R---C3---H3S
ATOM H3S  HAL2   0.09 !         |
GROUP                 !
ATOM C4   CTL2  -0.18 !         |
ATOM H4R  HAL2   0.09 !  H4R---C4---H4S
ATOM H4S  HAL2   0.09 !         |
GROUP                 !
ATOM C5   CTL2  -0.18 !         |
ATOM H5R  HAL2   0.09 !  H5R---C5---H5S
ATOM H5S  HAL2   0.09 !         |
GROUP                 !
ATOM C6   CTL2  -0.18 !         |
ATOM H6R  HAL2   0.09 !  H6R---C6---H6S
ATOM H6S  HAL2   0.09 !         |
GROUP                 !
ATOM C7   CTL2  -0.18 !         |
ATOM H7R  HAL2   0.09 !  H7R---C7---H7S
ATOM H7S  HAL2   0.09 !         |
GROUP                 !
ATOM C8   CTL2  -0.18 !         |
ATOM H8R  HAL2   0.09 !  H8R---C8---H8S
ATOM H8S  HAL2   0.09 !         |
GROUP                 !
ATOM C9   CTL2  -0.18 !         |
ATOM H9R  HAL2   0.09 !  H9R---C9---H9S
ATOM H9S  HAL2   0.09 !         |
GROUP                 !
ATOM C10  CTL3  -0.27 !         |
ATOM H10S HAL3   0.09 ! H10R---C10--H10S
ATOM H10R HAL3   0.09 !         |
ATOM H10T HAL3   0.09 !        H10T

BOND  O1  C1
BOND  C1  C2
DOUBLE  C1  O2
BOND  C2  H2R       C2  H2S       C2  C3
BOND  C3  H3R       C3  H3S       C3  C4
BOND  C4  H4R       C4  H4S       C4  C5
BOND  C5  H5R       C5  H5S       C5  C6
BOND  C6  H6R       C6  H6S       C6  C7
BOND  C7  H7R       C7  H7S       C7  C8
BOND  C8  H8R       C8  H8S       C8  C9
BOND  C9  H9R       C9  H9S       C9  C10
BOND  C10 H10R      C10 H10S      C10 H10T

IMPR C1 O1 C2 O2

end

return

dca.pdb

REMARK  READS THE DCA RESIDUE FROM THE STREAM TOPOLOGY FILE AND WRITES A PDB CONSISTIN
REMARK  OF A SINGLE DCA MOLECULE                                                      
REMARK   DATE:     2/ 8/24     11:35:17      CREATED BY USER: thomas                  
ATOM      1  H1  DECA    1      -1.447  -1.387  -0.000  1.00  0.00      DECA
ATOM      2  O1  DECA    1      -0.490  -1.311  -0.000  1.00  0.00      DECA
ATOM      3  O2  DECA    1      -0.726   0.981  -0.000  1.00  0.00      DECA
ATOM      4  C1  DECA    1       0.000   0.000   0.000  1.00  0.00      DECA
ATOM      5  C2  DECA    1       1.522   0.000   0.000  1.00  0.00      DECA
ATOM      6  H2R DECA    1       1.893  -0.524   0.907  1.00  0.00      DECA
ATOM      7  H2S DECA    1       1.893   1.047  -0.000  1.00  0.00      DECA
ATOM      8  C3  DECA    1       1.995   1.455   0.000  1.00  0.00      DECA
ATOM      9  H3R DECA    1       1.617   1.979  -0.904  1.00  0.00      DECA
ATOM     10  H3S DECA    1       3.105   1.496   0.000  1.00  0.00      DECA
ATOM     11  C4  DECA    1       3.517   1.604   0.000  1.00  0.00      DECA
ATOM     12  H4R DECA    1       3.948   1.122   0.904  1.00  0.00      DECA
ATOM     13  H4S DECA    1       3.796   2.680   0.000  1.00  0.00      DECA
ATOM     14  C5  DECA    1       3.990   3.060   0.000  1.00  0.00      DECA
ATOM     15  H5R DECA    1       3.612   3.584  -0.904  1.00  0.00      DECA
ATOM     16  H5S DECA    1       5.101   3.100   0.000  1.00  0.00      DECA
ATOM     17  C6  DECA    1       5.513   3.209   0.000  1.00  0.00      DECA
ATOM     18  H6R DECA    1       5.944   2.727   0.904  1.00  0.00      DECA
ATOM     19  H6S DECA    1       5.791   4.284  -0.000  1.00  0.00      DECA
ATOM     20  C7  DECA    1       5.986   4.664   0.000  1.00  0.00      DECA
ATOM     21  H7R DECA    1       5.608   5.188  -0.904  1.00  0.00      DECA
ATOM     22  H7S DECA    1       7.096   4.705   0.000  1.00  0.00      DECA
ATOM     23  C8  DECA    1       7.508   4.813   0.000  1.00  0.00      DECA
ATOM     24  H8R DECA    1       7.939   4.331   0.904  1.00  0.00      DECA
ATOM     25  H8S DECA    1       7.787   5.889   0.000  1.00  0.00      DECA
ATOM     26  C9  DECA    1       7.981   6.268   0.000  1.00  0.00      DECA
ATOM     27  H9R DECA    1       7.603   6.793  -0.904  1.00  0.00      DECA
ATOM     28  H9S DECA    1       9.092   6.309   0.000  1.00  0.00      DECA
ATOM     29  C10 DECA    1       9.498   6.455   0.000  1.00  0.00      DECA
ATOM     30 H10S DECA    1       9.940   5.983   0.904  1.00  0.00      DECA
ATOM     31 H10R DECA    1       9.750   7.537   0.000  1.00  0.00      DECA
ATOM     32 H10T DECA    1       9.940   5.983  -0.904  1.00  0.00      DECA
TER      33      DECA     1
END

vmd visualised pdb file

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2
  • $\begingroup$ Can you try hbuild sele all? This should build your hydrogens automatically, and you can also do a short energy minimization followed by that. $\endgroup$ Commented Feb 16 at 19:08
  • $\begingroup$ Did the answer fix your problem? If yes, please mark the answer as accepted. $\endgroup$ Commented Feb 21 at 0:39

2 Answers 2

2
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I was able to build the structure correctly using the following input file

* Reads the DCA residue from the stream topology file and writes a pdb consisting
* of a single DCA molecule
*

bomlev -5
wrnlev -5

!topology and parameter files
open read card unit 10 name toppar/top_all36_lipid.rtf
read  rtf card unit 10 

open read card unit 20 name toppar/par_all36_lipid.prm
read para card unit 20 flex

stream top_test.str

read sequence DECA 1
generate DECA

!read sequence DECN 1
!generate DECN

ic generate
ic param
ic seed 1 C1 1 C2 1 C3 !to generate box CHARMM must know coords of at least three atoms defined by top file
ic build
print ic

coor build
coor print
hbuild sele all end

mini sd 10000 1000

open write card unit 30 name DCA_build.pdb
write coor pdb  unit 30
close unit 30

Coordinates

REMARK  READS THE DCA RESIDUE FROM THE STREAM TOPOLOGY FILE AND WRITES A PDB CONSISTIN
REMARK  OF A SINGLE DCA MOLECULE                                                      
REMARK   DATE:     2/16/24     12:33:46      CREATED BY USER: hemanthharid            
ATOM      1  H1  DECA    1      -1.205  -1.285  -0.209  1.00  0.00      DECA
ATOM      2  O1  DECA    1      -0.275  -1.216   0.005  1.00  0.00      DECA
ATOM      3  O2  DECA    1      -0.760   0.944  -0.357  1.00  0.00      DECA
ATOM      4  C1  DECA    1       0.065   0.124  -0.030  1.00  0.00      DECA
ATOM      5  C2  DECA    1       1.493   0.398   0.469  1.00  0.00      DECA
ATOM      6  H2R DECA    1       2.017  -0.561   0.654  1.00  0.00      DECA
ATOM      7  H2S DECA    1       1.364   0.914   1.445  1.00  0.00      DECA
ATOM      8  C3  DECA    1       2.368   1.305  -0.442  1.00  0.00      DECA
ATOM      9  H3R DECA    1       1.739   2.078  -0.937  1.00  0.00      DECA
ATOM     10  H3S DECA    1       2.842   0.692  -1.241  1.00  0.00      DECA
ATOM     11  C4  DECA    1       3.457   2.026   0.384  1.00  0.00      DECA
ATOM     12  H4R DECA    1       4.062   1.263   0.921  1.00  0.00      DECA
ATOM     13  H4S DECA    1       2.949   2.655   1.150  1.00  0.00      DECA
ATOM     14  C5  DECA    1       4.411   2.930  -0.423  1.00  0.00      DECA
ATOM     15  H5R DECA    1       3.812   3.691  -0.971  1.00  0.00      DECA
ATOM     16  H5S DECA    1       4.945   2.312  -1.178  1.00  0.00      DECA
ATOM     17  C6  DECA    1       5.452   3.658   0.460  1.00  0.00      DECA
ATOM     18  H6R DECA    1       6.061   2.899   1.000  1.00  0.00      DECA
ATOM     19  H6S DECA    1       4.921   4.273   1.219  1.00  0.00      DECA
ATOM     20  C7  DECA    1       6.396   4.565  -0.351  1.00  0.00      DECA
ATOM     21  H7R DECA    1       5.792   5.306  -0.920  1.00  0.00      DECA
ATOM     22  H7S DECA    1       6.927   3.926  -1.093  1.00  0.00      DECA
ATOM     23  C8  DECA    1       7.466   5.329   0.460  1.00  0.00      DECA
ATOM     24  H8R DECA    1       8.044   4.605   1.075  1.00  0.00      DECA
ATOM     25  H8S DECA    1       6.982   6.052   1.153  1.00  0.00      DECA
ATOM     26  C9  DECA    1       8.422   6.058  -0.507  1.00  0.00      DECA
ATOM     27  H9R DECA    1       7.863   6.878  -1.012  1.00  0.00      DECA
ATOM     28  H9S DECA    1       8.689   5.315  -1.294  1.00  0.00      DECA
ATOM     29  C10 DECA    1       9.740   6.616   0.050  1.00  0.00      DECA
ATOM     30 H10S DECA    1      10.038   6.119   0.996  1.00  0.00      DECA
ATOM     31 H10R DECA    1       9.675   7.712   0.222  1.00  0.00      DECA
ATOM     32 H10T DECA    1      10.551   6.446  -0.695  1.00  0.00      DECA
TER      33      DECA     1
END

This is the structure that OP generated enter image description here

You can clearly see that the hydrogens are oriented along the C-C bond axis, which in turn causes the extra bonds that OP complained about.

Now, the structure that I generated using the input provided below enter image description here

The hydrogens are oriented properly now.

Conclusion: VMD was not the problem, instead the coordinates generated by OP was the problem.

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-1
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I was able to resolve this by simply including a psf alongside a cor file when visualising in vmd. I got an answer from the charmm forums. Apparently vmd will attempt to bond hydrogens itself if there is no data on bonds. Including the psf fixes it.

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2
  • $\begingroup$ Can you please show us the answer at the CHARMM forum? $\endgroup$ Commented Feb 27 at 11:05
  • 1
    $\begingroup$ I agree that including PSF file will solve the problem of extra bonds, but that still does not solve the problem of incorrect coordinates for hydrogens. You literally have hydrogen atoms along the C-C bonds, which is wrong, and this is causing the issue with extra bonds. $\endgroup$ Commented Feb 27 at 17:19

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