Dear users,
I am a beginner in lammps. I am trying to simulate alanine dipeptide. I got the pdf and psf files from NAMD tutorials. I used the perl script charmm2lammps.pl which uses pdb, psf, topology and parameter files as inputs and generates lammps input files. (I am using par_all36_prot.prm and top_all36_prot.rtf as inputs for perl script (all36_prot as forcefield input)).
Problem: the data file generated has the following lines:
22 atoms
21 bonds
36 angles
41 dihedrals
4 impropers
2 atom types
0 bond types
0 angle types
0 dihedral types
0 improper types
which are wrong for alanine dipeptide. (8 atom types should be there and many bond, angle, dihedral types)
I also loaded the pdb and psf files in vmd and used topotools to write lammps data files, which also generated wrong information :
22 atoms
21 bonds
36 angles
41 dihedrals
4 impropers
8 atom types
1 bond types
1 angle types
1 dihedral types
1 improper types
Please help me in letting me know what I am doing wrong here.
Thanks,
Madhur
this is all useless without providing more details:
-
the versions of the respective software used
-
the files used
-
the commands or scripts used
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the platform (OS, CPU architecture) you are running on.
axel.
Hi Sir,
Sorry not to specify all the relevant details earlier. I have used the par_all36_prot.prm and top_all36_prot.rtf files available in the tools/ch2lmp/example-cmap folder (attached).
Command used : perl charmm2lammps.pl all36_prot A
Perl version : v5.22.1
CPU architecture : x86_64
OS : Ubuntu 16.04.2 LTS xenial
I have attached the full data file I obtained this time, here's the starting few lines of the data file.
22 atoms
21 bonds
36 angles
43 dihedrals
4 impropers
8 atom types
10 bond types
20 angle types
28 dihedral types
4 improper types
I got some bond, angles, dihedral types this time. I must have used topology and parameter files from some other source earlier, which gave me even worse results in the data file produced earlier. But, running these files also gave me some warnings (copied below), which is why my data file is still not correct.
Terminal output and Warnings :
charmm2lammps v1.9.1 (c)2005-2016
Info: using A.pdb instead of A.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 [ CT1 ] was not found
Warning: bond parameter 8 for [CT3 HA ] was not found
Info: converting angles
Warning: angle parameter 1 for [ CT1 C ] was not found
Warning: angle parameter 2 for [ CT1 CT3 ] was not found
Warning: angle parameter 3 for [ CT1 NH1 ] was not found
Warning: angle parameter 6 for [C CT3 HA ] was not found
Warning: angle parameter 12 for [CT1 CT3 HA ] was not found
Warning: angle parameter 18 for [HA CT3 HA ] was not found
Warning: angle parameter 19 for [HA CT3 NH1 ] was not found
Info: converting dihedrals
Warning: dihedral parameter 1 for [ CT1 C NH1 ] was not found
Warning: dihedral parameter 2 for [ CT1 C O ] was not found
Warning: dihedral parameter 3 for [ CT1 CT3 HA ] was not found
Warning: dihedral parameter 4 for [ CT1 NH1 C ] was not found
Warning: dihedral parameter 5 for [ CT1 NH1 H ] was not found
Warning: dihedral parameter 10 for [C NH1 CT3 HA ] was not found
Warning: dihedral parameter 21 for [H NH1 CT3 HA ] was not found
Warning: dihedral parameter 22 for [HA CT3 C NH1 ] was not found
Warning: dihedral parameter 23 for [HA CT3 C O ] was not found
Info: converting impropers
Info: conversion complete
I think there's something wrong in my topology and parameter files. Please help me to figure out what I should do so that these warnings disappear and I generate a correct data file.
Regards,
Madhur
par_all36_prot.prm (181 KB)
charmm2lammps.pl (70.5 KB)
A.psf (4.83 KB)
A.pdb (1.77 KB)
A.data (13.4 KB)
top_all36_prot.rtf (71.5 KB)
Hi Sir,
Sorry not to specify all the relevant details earlier. I have used the
par_all36_prot.prm and top_all36_prot.rtf files available in the
tools/ch2lmp/example-cmap folder (attached).
Command used : perl charmm2lammps.pl all36_prot A
Perl version : v5.22.1
CPU architecture : x86_64
OS : Ubuntu 16.04.2 LTS xenial
thanks for the info.
[...]
I think there's something wrong in my topology and parameter files. Please
help me to figure out what I should do so that these warnings disappear and
I generate a correct data file.
the issue is, that your .psf file was created with/for a different (older)
version of the CHARMM force field (CHARMM22?) and thus it is using atom
types that are no longer available in CHARMM36, which confuses the
charmm2lammps.pl script. you can see which atom types are affected, by
checking the comments in the atoms section and comparing them to the psf
file.
check this out:
Atoms # full
1 1 6 -0.27 4.684 -0.562
14.838 # CT3
2 1 3 0.09 4.03 -1.401
14.524 # HA
3 1 3 0.09 4.14 0.399
14.716 # HA
4 1 3 0.09 4.944 -0.692
15.912 # HA
5 1 4 0.51 5.926 -0.549
14.036 # C
6 1 8 -0.51 7.027 -0.604
14.566 # O
7 1 7 -0.47 5.782 -0.465
12.709 # NH1
8 1 2 0.31 4.878 -0.403
12.305 # H
9 1 5 0.07 6.901 -0.466
11.787 # CT1
10 1 1 0.09 7.656 -1.148
12.157 #
11 1 6 -0.27 6.425 -0.97
10.409 # CT3
12 1 3 0.09 5.663 -0.283
9.982 # HA
13 1 3 0.09 7.278 -1.026
9.698 # HA
14 1 3 0.09 5.98 -1.982
10.503 # HA
so, the atom type for atom 10 is not recognized. checking the parameter
file and topology file entry for ALA, one can see that this should be atom
type HB1 instead of HB
but it does not stop there. also type HA is not correct anymore; it should
be HA3.
the unmodified .psf file does convert without a problem using the
equivalent CHARMM27 topology and parameter files.
thus i suggest you redo the psf file generation for the CHARMM force field
version that you want to use with charmm2lammps.pl
axel.