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leelasd / ligpargen

A repository for tutorials and FAQ's about LigParGen
http://traken.chem.yale.edu/ligpargen/
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Problemst in creating itp file for acetonitrile(CH3CN) #74

Open NaviChemist opened 3 years ago

NaviChemist commented 3 years ago

Good morning! Unfortanutelly, I am not able to create itp and gro file for acetonitrile. I used several variants for that, using pdb file, smile code created in draw molecula soft on your site. (CC#N and even I tried to do it like N#CC, or N#CC[D])(I need it for OPLS-AA) I dont know what is the problem, please have a look at this problem. In any case you can contact me by email sim1998@mail.ru. Have a nice day!

therealchrisneale commented 3 years ago

CC#N works in the command line version. Here is the output I got for the gromacs .itp file and the .pdb file:

########################## $ cat CC#N.itp

; Writted by Leela S. Dodda leela.dodda@yale.edu ; GENERATED BY Server ; Jorgensen Lab @ Yale University ; [ atomtypes ] opls_801 C801 12.0110 0.000 A 3.30000E-01 2.76144E-01 opls_805 H805 1.0080 0.000 A 2.50000E-01 1.25520E-01 opls_803 H803 1.0080 0.000 A 2.50000E-01 1.25520E-01 opls_800 C800 12.0110 0.000 A 3.50000E-01 2.76144E-01 opls_804 H804 1.0080 0.000 A 2.50000E-01 1.25520E-01 opls_802 N802 14.0070 0.000 A 3.20000E-01 7.11280E-01 [ moleculetype ] ; Name nrexcl UNK 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass
1 opls_800 1 UNK C00 1 -0.1422 12.0110 2 opls_801 1 UNK C01 1 0.1564 12.0110 3 opls_802 1 UNK N02 1 -0.38659999999999994 14.0070 4 opls_803 1 UNK H03 1 0.1241 1.0080 5 opls_804 1 UNK H04 1 0.1241 1.0080 6 opls_805 1 UNK H05 1 0.1241 1.0080 [ bonds ] 2 1 1 0.1470 326352.000 3 2 1 0.1157 543920.000 4 1 1 0.1090 284512.000 5 1 1 0.1090 284512.000 6 1 1 0.1090 284512.000

[ angles ] ; ai aj ak funct c0 c1 c2 c3 1 2 3 1 180.000 1255.200 2 1 4 1 108.500 292.880 2 1 5 1 108.500 292.880 2 1 6 1 108.500 292.880 4 1 5 1 107.800 276.144 4 1 6 1 107.800 276.144 5 1 6 1 107.800 276.144

[ dihedrals ] ; IMPROPER DIHEDRAL ANGLES ; ai aj ak al funct c0 c1 c2 c3 c4 c5

[ dihedrals ] ; PROPER DIHEDRAL ANGLES ; ai aj ak al funct c0 c1 c2 c3 c4 c5 4 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 5 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000 6 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000

[ pairs ] 3 4 1 3 5 1 3 6 1

########################## $ cat CC#N.pdb

REMARK LIGPARGEN GENERATED PDB FILE ATOM 1 C00 UNK 1 1.000 1.000 0.000 ATOM 2 C01 UNK 1 -0.461 1.000 0.000 ATOM 3 N02 UNK 1 -1.622 1.000 0.001 ATOM 4 H03 UNK 1 1.389 0.002 -0.225 ATOM 5 H04 UNK 1 1.389 1.303 0.976 ATOM 6 H05 UNK 1 1.388 1.696 -0.751 TER CONECT 1 2 CONECT 2 3 CONECT 1 4 CONECT 1 5 CONECT 1 6

brbvisayas commented 3 years ago

Hi, I have come across the same issue with the CC#N in both the web and in the command line version. I was wondering how you got the command line version to give you the parameters. I was getting "ZeroDivisionError: float division by zero" errors. Benzene and DMSO worked for me but not acetonitrile. I was hoping to get the parameters for a LAMMPS simulation.