Issues with perl scripting to write data files

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1

Hello everyone,

I am trying to run a simulation which contains protein system and a carbohydrate system. As mentioned in one of the lammps-user emails, I have combined the CHARMM topology and parameter file to create the psf file for my system. The system thus created runs perfectly well in NAMD. But when I am using the same merged topology and parameter file to create lammps data file, perl script cannot read the protein component of the pdb and psf file, and the protein part is being shown as atom type 1.

It is also showing the following error

Info: using Tc1comp.pdb instead of Tc1comp.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
Warning: dihedral parameter 1 for [ ] was not found
Info: converting impropers
Warning: improper parameter 1 for [ ] was not found
Info: conversion complete

Can anyone help me regarding this?

P.s. The PDB PSF file along with the merged topology and parameter file runs perfectly well in NAMD.

2

if i remember correctly, NAMD uses x-plor style .psf files while the converter perl script in LAMMPS expects CHARMM format files. there should be a way to make psfgen from NAMD output CHARMM style psf files.

axel.

3

Axel,

Even with the X-plor style .psf files, I can create lammps data files individually for protein and carbohydrate using their respective topology and parameter files.

The problem arises when I merge the two PDB and PSF files along-with topology and parameter files

The individual protein and carbohydrate data files run perfectly well in LAMMPS.

The data file created looks like this

Masses

1 0 #

2 22.98977 # SOD

3 12.011 # CC3161

4 12.011 # CC3162

5 12.011 # CC3163

6 12.011 # CC321

7 12.011 # CC331

8 12.011 # CC2O1

9 12.011 # CC2O2

10 1.008 # HCA1

11 1.008 # HCA2

12 1.008 # HCA3

13 1.008 # HCP1

14 15.9994 # OC311

15 15.9994 # OC3C61

16 15.9994 # OC2D1

17 15.9994 # OC2D2

18 14.007 # NC2D1

The atom type 1 has 0 mass and all the protein atoms are shown as atom type 1.

If Perl expects CHARMM style psf files, then even the data files of individual protein and carbohydrate systems would not be created.

4

which version of LAMMPS are you using?

the strange entry for atom type 1 means, that there is something in your psf, that the converter script cannot parse correctly.

axel.