Problem in bond and angle parameter in forming topology file

LAMMPS LAMMPS General Discussion
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1

We are making a topology file using the perl command for Charmm2lammps conversion. In that case, for POPC, it only takes the top & par lipid file and by master file also. If we add water then we cann’t make it. Then we created master file by adding parameter file of lipid, carbohydrades, protein & cgenff. If we add the parameters of water then it is showing-

Info: using wp_edited.pdb instead of wp_edited.crd
Info: lx not set: will use extremes
Info: ly not set: will use extremes
Info: lz not set: will use extremes
Info: creating PSF index
Info: converting atoms
Info: converting bonds
Warning: bond parameter 1 for [ ] was not found
Info: converting angles
Warning: angle parameter 1 for [ ] was not found
Info: converting dihedrals
Info: converting impropers
Info: conversion complete,

if we took the par & top file of water ions in the old version and made the pgn file only for water then it is working but when we copy those parameters in the master file along with others and we made the pgn file for POPC and water then again it is not working.

2

Your post is missing a lot of information – “it is not working” could be anything from “the simulation gives an area per lipid that is too small” to “the simulation crashed my computer and nearly burned down the office”.

At a bare minimum, giving us an error message tells us very concretely when something “is not working” and enables both us and yourself to investigate further. For example, the one error message you have included shows quite clearly that the Perl script you are using fails to find the bond and angle parameters of water, which in turn could have any number of causes (improper CHARMM input, or no force constants due to using a rigid water model, or …).

In any case, this sounds like a problem of either your CHARMM input or the Perl script. I’m not familiar with either and I doubt most of the forum users here are either. You may have better luck on the CHARMM forums, or on “Science Talk” or other online forums, and always ask your supervisor for advice and instructions. All the best!

3

It is not working means sometime in the data file which is generated, it is not taking all the atom types of POPC or sometime in case of PAH4 , it is not counting the coordinate of the PHE portion. Actually we are trying to make topology file for a water desalination system using bio-membrane (PAH4)…
the water and POPC combined data file…
" 18 atom types
22 bond types
42 angle types
88 dihedral types
1 improper types

  -1.402        58.99 xlo xhi
  -0.033       62.429 ylo yhi
     -25           70 zlo zhi

Masses

   1          0  #
   2      1.008  # HL
   3      1.008  # HAL1
   4      1.008  # HAL2
   5      1.008  # HAL3
   6      1.008  # HEL1
   7     12.011  # CL
   8     12.011  # CTL1
   9     12.011  # CTL2
  10     12.011  # CTL3
  11     12.011  # CTL5                        ''

the PAH4 data file-
"
Masses

   1      1.008
   2      1.008
   3      1.008
   4      1.008
   5     12.011
   6     12.011
   7     12.011
   8     12.011
   9     12.011
  10     14.007
  11     15.999
  12     15.999
  13     15.999
  14          0
  15          0
  16          0
  17          0
  18          0
  19          0
  20          0
  21          0
  22          0
  23          0
  24          0
  25          0                                  "

Pair Coeffs

and …
‘’ 253 1 10 -0.47 25.954 34.71 11.514
254 1 1 0.31 24.988 34.736 11.764
255 1 7 0.07 26.154 35.172 10.085
256 1 3 0.09 27.213 35.331 9.953
257 1 8 -0.18 25.526 36.557 9.788
258 1 4 0.09 0 0 0
259 1 4 0.09 0 0 0
260 1 6 0 25.98 37.137 8.356
261 1 6 -0.115 0 0 0
262 1 2 0.115 0 0 0
263 1 6 -0.115 0 0 0
264 1 2 0.115 0 0 0
265 1 6 -0.115 26.892 38.201 5.953
266 1 2 0.115 27.345 38.464 5.008
267 1 6 -0.115 0 0 0
268 1 2 0.115 0 0 0
269 1 6 -0.115 0 0 0
270 1 2 0.115 0 0 0
271 1 5 0.51 25.835 34.062 8.963
272 1 11 -0.51 28.06 35.254 12.228
273 1 10 -0.47 0 0 0
274 1 1 0.31 0 0 0
275 1 7 0.07 0 0 0
276 1 3 0.09 0 0 0
277 1 8 -0.18 0 0 0
278 1 4 0.09 0 0 0
279 1 4 0.09 0 0 0
280 1 6 0 0 0 0
281 1 6 -0.115 0 0 0
282 1 2 0.115 0 0 0 "

4

I think this is the key here. The charmm2lammps script predates CGENFF by a long margin and thus cannot handle that the names are longer and thus does not process the types correctly.

You can try renaming the types in psf and force field file to see if you can make it work, but my hopes are not very high that this will work sufficiently well.

5

If you have a procedure that works entirely without water, I’d suggest using that first for the data file. Then generate a water-only data file and add that to the first data file in LAMMPS using the read_data command with add option.

6

In the phenyl alanine portion it is not counting the coordinate…
250 1 1 0.09 25.893 35.64 21.016
251 1 1 0.09 26.042 33.927 20.752
252 1 1 -0.511 28.721 35.377 19.898
253 1 11 -0.47 33.964 29.946 35.73
254 1 2 0.31 0 0 0
255 1 8 0.07 0 0 0
256 1 4 0.09 0 0 0
257 1 9 -0.18 0 0 0
258 1 5 0.09 0 0 0
259 1 5 0.09 0 0 0
260 1 7 0 0 0 0
261 1 7 -0.115 0 0 0
262 1 3 0.115 0 0 0
263 1 7 -0.115 0 0 0
264 1 3 0.115 0 0 0
265 1 7 -0.115 0 0 0
266 1 3 0.115 0 0 0
267 1 7 -0.115 0 0 0
268 1 3 0.115 0 0 0
269 1 7 -0.115 0 0 0
270 1 3 0.115 0 0 0
271 1 6 0.51 0 0 0
272 1 12 -0.51 0 0 0

7

In that case we only took only the PAH4, made the .pgn file file-
‘’
package require psfgen
topology top_rajib.rtf

segment PAH4 {
auto none
pdb pah4_b.pdb
first NONE
last NONE
}
coordpdb pah4_b.pdb PAH4
guesscoord

writepdb pah4_edited.pdb
writepsf pah4_edited.psf
‘’

8

This is psfgen code from NAMD/VMD.

The real problem is, however, can charmm2lammps.pl properly parse the atom types and find them in the provided force field files?

As already pointed out, the converter tool predates some recent development and changes in CHARMM and thus you have to make certain that your input does conform with the expectations of the converter, not psfgen.

You have not provided any details or evidence in that respect, so there is no advice beyond what was already given.