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 filesstream toppar.strread sequence DECA 1generate DECA!read sequence DECN 1!generate DECNic generateic paramic seed 1 C1 1 C2 1 C3 !to generate box CHARMM must know coords of at least three atoms defined by top fileic buildopen write card unit 10 name DCA_build.pdbwrite coor pdb unit 10top_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 1AUTOGENERATE ANGLE DIHERESI DECA 0.00 ! Decanoic Acid (10:0)GROUP !ATOM H1 HOL 0.44 !ATOM O1 OHL -0.61 ! O2 O1--H1ATOM O2 OBL -0.55 ! \\ /ATOM C1 CL 0.75 ! C1ATOM C2 CTL2 -0.21 ! |ATOM H2R HAL2 0.09 ! H2R---C2---H2SATOM H2S HAL2 0.09 ! | GROUP !ATOM C3 CTL2 -0.18 ! |ATOM H3R HAL2 0.09 ! H3R---C3---H3SATOM H3S HAL2 0.09 ! |GROUP !ATOM C4 CTL2 -0.18 ! |ATOM H4R HAL2 0.09 ! H4R---C4---H4SATOM H4S HAL2 0.09 ! |GROUP !ATOM C5 CTL2 -0.18 ! |ATOM H5R HAL2 0.09 ! H5R---C5---H5SATOM H5S HAL2 0.09 ! |GROUP !ATOM C6 CTL2 -0.18 ! |ATOM H6R HAL2 0.09 ! H6R---C6---H6SATOM H6S HAL2 0.09 ! |GROUP !ATOM C7 CTL2 -0.18 ! |ATOM H7R HAL2 0.09 ! H7R---C7---H7SATOM H7S HAL2 0.09 ! |GROUP !ATOM C8 CTL2 -0.18 ! |ATOM H8R HAL2 0.09 ! H8R---C8---H8SATOM H8S HAL2 0.09 ! |GROUP !ATOM C9 CTL2 -0.18 ! |ATOM H9R HAL2 0.09 ! H9R---C9---H9SATOM H9S HAL2 0.09 ! |GROUP !ATOM C10 CTL3 -0.27 ! |ATOM H10S HAL3 0.09 ! H10R---C10--H10SATOM H10R HAL3 0.09 ! |ATOM H10T HAL3 0.09 ! H10TBOND O1 H1BOND O1 C1BOND C1 C2DOUBLE C1 O2BOND C2 H2R C2 H2S C2 C3BOND C3 H3R C3 H3S C3 C4BOND C4 H4R C4 H4S C4 C5BOND C5 H5R C5 H5S C5 C6BOND C6 H6R C6 H6S C6 C7BOND C7 H7R C7 H7S C7 C8BOND C8 H8R C8 H8S C8 C9BOND C9 H9R C9 H9S C9 C10BOND C10 H10R C10 H10S C10 H10TIMPR C1 O1 C2 O2RESI DECN -1.00 ! Decanoic acid (10:0), unprotonatedGROUP !ATOM O1 OCL -0.76 ! O2 O1 (-)ATOM O2 OCL -0.76 ! \\ /ATOM C1 CL 0.62 ! C1ATOM C2 CTL2 -0.28 ! |ATOM H2R HAL2 0.09 ! H2R---C2---H2SATOM H2S HAL2 0.09 ! | GROUP !ATOM C3 CTL2 -0.18 ! |ATOM H3R HAL2 0.09 ! H3R---C3---H3SATOM H3S HAL2 0.09 ! |GROUP !ATOM C4 CTL2 -0.18 ! |ATOM H4R HAL2 0.09 ! H4R---C4---H4SATOM H4S HAL2 0.09 ! |GROUP !ATOM C5 CTL2 -0.18 ! |ATOM H5R HAL2 0.09 ! H5R---C5---H5SATOM H5S HAL2 0.09 ! |GROUP !ATOM C6 CTL2 -0.18 ! |ATOM H6R HAL2 0.09 ! H6R---C6---H6SATOM H6S HAL2 0.09 ! |GROUP !ATOM C7 CTL2 -0.18 ! |ATOM H7R HAL2 0.09 ! H7R---C7---H7SATOM H7S HAL2 0.09 ! |GROUP !ATOM C8 CTL2 -0.18 ! |ATOM H8R HAL2 0.09 ! H8R---C8---H8SATOM H8S HAL2 0.09 ! |GROUP !ATOM C9 CTL2 -0.18 ! |ATOM H9R HAL2 0.09 ! H9R---C9---H9SATOM H9S HAL2 0.09 ! |GROUP !ATOM C10 CTL3 -0.27 ! |ATOM H10S HAL3 0.09 ! H10R---C10--H10SATOM H10R HAL3 0.09 ! |ATOM H10T HAL3 0.09 ! H10TBOND O1 C1BOND C1 C2DOUBLE C1 O2BOND C2 H2R C2 H2S C2 C3BOND C3 H3R C3 H3S C3 C4BOND C4 H4R C4 H4S C4 C5BOND C5 H5R C5 H5S C5 C6BOND C6 H6R C6 H6S C6 C7BOND C7 H7R C7 H7S C7 C8BOND C8 H8R C8 H8S C8 C9BOND C9 H9R C9 H9S C9 C10BOND C10 H10R C10 H10S C10 H10TIMPR C1 O1 C2 O2endreturndca.pdb
REMARK READS THE DCA RESIDUE FROM THE STREAM TOPOLOGY FILE AND WRITES A PDB CONSISTINREMARK 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 DECAATOM 2 O1 DECA 1 -0.490 -1.311 -0.000 1.00 0.00 DECAATOM 3 O2 DECA 1 -0.726 0.981 -0.000 1.00 0.00 DECAATOM 4 C1 DECA 1 0.000 0.000 0.000 1.00 0.00 DECAATOM 5 C2 DECA 1 1.522 0.000 0.000 1.00 0.00 DECAATOM 6 H2R DECA 1 1.893 -0.524 0.907 1.00 0.00 DECAATOM 7 H2S DECA 1 1.893 1.047 -0.000 1.00 0.00 DECAATOM 8 C3 DECA 1 1.995 1.455 0.000 1.00 0.00 DECAATOM 9 H3R DECA 1 1.617 1.979 -0.904 1.00 0.00 DECAATOM 10 H3S DECA 1 3.105 1.496 0.000 1.00 0.00 DECAATOM 11 C4 DECA 1 3.517 1.604 0.000 1.00 0.00 DECAATOM 12 H4R DECA 1 3.948 1.122 0.904 1.00 0.00 DECAATOM 13 H4S DECA 1 3.796 2.680 0.000 1.00 0.00 DECAATOM 14 C5 DECA 1 3.990 3.060 0.000 1.00 0.00 DECAATOM 15 H5R DECA 1 3.612 3.584 -0.904 1.00 0.00 DECAATOM 16 H5S DECA 1 5.101 3.100 0.000 1.00 0.00 DECAATOM 17 C6 DECA 1 5.513 3.209 0.000 1.00 0.00 DECAATOM 18 H6R DECA 1 5.944 2.727 0.904 1.00 0.00 DECAATOM 19 H6S DECA 1 5.791 4.284 -0.000 1.00 0.00 DECAATOM 20 C7 DECA 1 5.986 4.664 0.000 1.00 0.00 DECAATOM 21 H7R DECA 1 5.608 5.188 -0.904 1.00 0.00 DECAATOM 22 H7S DECA 1 7.096 4.705 0.000 1.00 0.00 DECAATOM 23 C8 DECA 1 7.508 4.813 0.000 1.00 0.00 DECAATOM 24 H8R DECA 1 7.939 4.331 0.904 1.00 0.00 DECAATOM 25 H8S DECA 1 7.787 5.889 0.000 1.00 0.00 DECAATOM 26 C9 DECA 1 7.981 6.268 0.000 1.00 0.00 DECAATOM 27 H9R DECA 1 7.603 6.793 -0.904 1.00 0.00 DECAATOM 28 H9S DECA 1 9.092 6.309 0.000 1.00 0.00 DECAATOM 29 C10 DECA 1 9.498 6.455 0.000 1.00 0.00 DECAATOM 30 H10S DECA 1 9.940 5.983 0.904 1.00 0.00 DECAATOM 31 H10R DECA 1 9.750 7.537 0.000 1.00 0.00 DECAATOM 32 H10T DECA 1 9.940 5.983 -0.904 1.00 0.00 DECATER 33 DECA 1END