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Thanks, Now, Solved!

I have tried to read a molecule with fftool and in several data formats but I encounter several issues:
The molecule is TFSI:

16

C          6.03034        4.09220        5.48886
F          5.37202        5.30065        5.36546
F          6.39135        3.89541        6.80769
F          7.16406        4.10454        4.69920
N          3.42469        2.54403        5.86881
C          0.86033        0.89196        5.97521
F          0.03319        0.14152        5.16196
F          0.14535        1.94693        6.50866
F          1.34449        0.09819        6.99698
S          4.93349        2.75026        4.95267
S          2.24665        1.53550        4.99964
O          5.62532        1.37952        5.01298
O          4.53998        2.86277        3.47122
O          1.78341        2.37997        3.80211
O          3.05533        0.41678        4.32326
H          3.00037        3.48797        6.01118

I created a .pdb and a .gzmat extension with obabel and a .zmat extension with molden. All give different errors.

$ fftool 10 files/TFSI.xyz -r 10
> density 10.000 mol/L  volume 1660.6 A^3
> molecule_file      species           nmol force_field      nbond source  charge
> Traceback (most recent call last):
  File "/Users/marcodigennaro/WORK/external_packages/fftool/fftool", line 2816, in <module>
    main()
  File "/Users/marcodigennaro/WORK/external_packages/fftool/fftool", line 2768, in main
    spec.append(mol(zfile, connect, box))
  File "/Users/marcodigennaro/WORK/external_packages/fftool/fftool", line 615, in __init__
    self.fromxyz(filename, connect, box)
  File "/Users/marcodigennaro/WORK/external_packages/fftool/fftool", line 882, in fromxyz
    self.name = tok[0]            # molecule name
IndexError: list index out of range

$ fftool 10 files/TFSI.pdb -r 10
> density 10.000 mol/L  volume 1660.6 A^3
> molecule_file      species           nmol force_field      nbond source  charge
>  warning: no force field for TFSI
> Traceback (most recent call last):
  File "/Users/marcodigennaro/WORK/external_packages/fftool/fftool", line 2816, in <module>
    main()
  File "/Users/marcodigennaro/WORK/external_packages/fftool/fftool", line 2772, in main
    .format(zfile, spec[i].name, spec[i].nmol, spec[i].ffile,
TypeError: unsupported format string passed to NoneType.__format__

$ fftool 10 files/TFSI.zmat -r 10
> density 10.000 mol/L  volume 1660.6 A^3
> molecule_file      species           nmol force_field      nbond source  charge
> Traceback (most recent call last):
  File "/Users/marcodigennaro/WORK/external_packages/fftool/fftool", line 2816, in <module>
    main()
  File "/Users/marcodigennaro/WORK/external_packages/fftool/fftool", line 2768, in main
    spec.append(mol(zfile, connect, box))
  File "/Users/marcodigennaro/WORK/external_packages/fftool/fftool", line 611, in __init__
    self.fromzmat(filename, connect)
  File "/Users/marcodigennaro/WORK/external_packages/fftool/fftool", line 696, in fromzmat
    self.zmat2cart(z)
  File "/Users/marcodigennaro/WORK/external_packages/fftool/fftool", line 754, in zmat2cart
    theta = math.acos(delx / math.sqrt(delx*delx + dely*dely))
ZeroDivisionError: float division by zero

How to get the right zmat format? In the example folder some files (eg. ethane) have leading atom index:

ethane

1  C3H
2  C3H  1  rCC
3  H    2  rCH  1  aHCC
4  H    1  rCH  2  aHCC  3   d1
5  H    2  rCH  1  aHCC  4   d2
6  H    1  rCH  2  aHCC  5   d1
7  H    2  rCH  1  aHCC  6   d2
8  H    1  rCH  2  aHCC  7   d1
...

others (eg. benzene) do not:

benzene

CA
CA  1  rCC
CA  2  rCC  1  120.00
CA  3  rCC  2  120.00  1   0
CA  4  rCC  3  120.00  2   0
CA  5  rCC  4  120.00  3   0
HA  1  rCH  2  120.00  3 180
HA  2  rCH  3  120.00  4 180
HA  3  rCH  4  120.00  5 180
HA  4  rCH  5  120.00  6 180
HA  5  rCH  6  120.00  1 180
HA  6  rCH  1  120.00  2 180
...

What is the correct format and how to obtain it?
In my case, I don't know the atom types in advance (TFSI is just and example).
Thank you

Good morning,

I am having some issue in understanding the units conversion from the GROMACS .itp file into the LAMMPS .ff one. Please correct me if I am wrong.
GROMACS adopts the following units:

sigma [nm] epsilon [kJ/mol] b_0 [nm] k_b [kJ mol-1 nm-2]

whereas LAMMPS, when units real key is used, has the following units:

sigma [Å] epsilon [kcal/mol] b_0 [Å] k_b [kcal mol-1 Å-2]

To give you an example the .itp file is like:

[ atomtypes ] opls_800 C800 12.0110 0.000 A 3.50000E-01 2.76144E-01, where [ atoms ] 1 opls_800 1 UNK C00 1 -0.0487 12.0110

Whereas .ff looks like:

ATOMS C00 C00 12.011 -0.0487 lj 3.50 0.27614

Here I see the conversion from nm to Å, but I don't see the conversion from kJ/mol to kcal/mol. I am quite sure that here I am missing something, but I don't what I am missing.

Furthermore the equation used by GROMACS to define the bonded interaction uses a 1/2 term as prefactor, whereas the one used by LAMMPS, when the bond_style harmonic key is used, don't. Which means that all the k_b terms should be divided by 200 (if we don't consider the kJ to kcal conversion) when converting from GROMACS ([kJ mol-1 nm-2]) to LAMMPS real units ([kcal mol-1 Å-2]). Whereas I get:

GROMACS .itp
[ bonds ] 2 1 1 0.1410 267776.000

LAMMPS .ff
BONDS O01 C00 harm 1.410 2677.8

I am probably missing something since the simulations I run give reasonable results, but I just wanted to be sure about why especially since I need to write a customized .ff file by hand and I don't want to use erroneous values/units.

Thanks.

Matteo

Hello all,

I have generated input files for OpenMM using fftool and my system contains more than 100000 atoms. When running OpenMM I get an error "ValueError: Misaligned residue name" and it points to the line of atom 100000.
The error is solved by manually removing one space from the front of the residue name for all residues after 99999.
Is it possible to include this on the code?

Thank you!

Do we need a warning message when generating an input file for LAMMPS and not for OpenMM?

  warning: atom name SiO1a too long for pdb in siosicmim+
  warning: atom name HCSi1 too long for pdb in siosicmim+
...

Master created config.pdb on the left, fftool-02/22/2019 on the right (runs in GROMACS directly)

Dear Agilio Padua,

I have been using fftool for preparing my MD simulations with LAMMPS. I recently fell prey to an unexpected effect due to the order of directives in the LAMMPS input scripts generated by fftool.
If one uses pair_style hybrid, the pair_modify settings (e.g., tail correction) don't seem to be stored in the binary restart file. This will lead to an unexpected, yet significant, drop in the density in a simulation.

I have submitted the issue to the LAMMPS-users mailing list (see link below), but it is yet unclear whether this is going to be resolved internally in LAMMPS. To avoid any possible issues and confusion I would suggest changing the order of the restart and pair_style/pair_modify directives in the LAMMPS input generation in fftool.

If you want I can create a corresponding pull request.

Cheers,

Frank

inquiry to the LAMMPS-users mailing list: https://sourceforge.net/p/lammps/mailman/message/35456160/

I am using your fftool to convert a xyz file to the lammps input files and ran into some trouble with the IMPROPER keyword in the ff file, it seems the code doesnt read it. Therefor the impropers get added to the list of dihedrals. Also the potential keyword isnt read for dihedral and defaults to opls. I have added the xyz and ff files for reference.

xyz.txt
ff.txt

Thank you for your time.

Is there a way for fftool to output to Amber? I tried to output to GROMACS first and then used Parmed to convert GROMACS topology to Amber but got the error that it couldn't identify the file format.

Hi, I was trying to simulate some carbonates, specifically propylene carbonate and ethylene carbonate and other not cyclic, but I can't find the parameters in the force field so that the molecules are neutral. The cyclic residuals with the respective parameters used among those present in the force field are:

  O_2                 O_2
  ||                  ||
  C_2               C_2
 /   \               /   \
OS   OS     OS   OS
 \   /               \   /
 CT-CT        CT-CT
         \           
          CT

propylencarbonate ethylencarbonate

Thank you for your time.