AMBER Archive (2001)

Subject: Re: saving a trajectory as individual pdb files

From: Jarrod Smith (jsmith_at_structbio.vanderbilt.edu)
Date: Mon Apr 02 2001 - 17:39:15 CDT

Jake Isaacs wrote:
>
> What is the best way to covert a trajectory into a series of pdb files? If
> more than one program is required, does anyone have a handy script I could
> modify for my purposes?

There are probably better tools for this, but below is some C code that will get the job done in one step. It may need to be tweaked if your
trajectory has box info in it. To use the prog, you need a pdb file of your system (created with ambpdb) and the trajectory file. 

-- 
Jarrod A. Smith
Research Asst. Professor, Biochemistry
Asst. Director, Center for Structural Biology
Computation and Molecular Graphics
Vanderbilt University
jsmith_at_structbio.vanderbilt.edu

#include <stdio.h>

#define USAGE   "usage: %s pdb_file trajectory_file\n", argv[ 0 ]
#define ERROR   -1
#define SUCCESS 0

#define MAX_ATOMS       50000
#define RNAME_SIZE      4
#define ANAME_SIZE      5

typedef struct{
   int   rnum, anum;
   char  rname[RNAME_SIZE], aname[ANAME_SIZE];
        float   coords[3];
}ATOM;

ATOM  atom[MAX_ATOMS];

char    line[100];

main(argc, argv)
int     argc;
char    *argv[];
{
        int     n_atoms, anum, frame=0, c;
        char    fname[256];
        float   f;
        FILE    *pdbFile, *trajFile;

        if (argc < 3) {
                fprintf( stderr, USAGE );
                exit (ERROR);
        }

        if ( (pdbFile = fopen( argv[ 1 ], "r")) == NULL ) {
                fprintf( stderr, "FATAL: Can't open pdb file %s\n", argv[ 1 ] );
                exit (ERROR);
        }else{
                n_atoms=make_atom_table( pdbFile );
                fprintf( stderr, "Found %d atoms in %s. Using this as framesize\n", argv[1]);
        }

        if ( (trajFile = fopen( argv[ 2 ], "r")) == NULL ) {
                fprintf( stderr, "FATAL: Can't open trajectory file %s\n", argv[ 2 ] );
                exit (ERROR);
   }
        fgets( line, sizeof(line), trajFile );
        fprintf(stderr, "\n");
        while( fscanf( trajFile, "%f", &atom[0].coords[0] ) == 1 ){
                frame++;
                sprintf( fname, "frame%03d.pdb", frame );
                fprintf( stderr, "Extracting frame %d to file %s...\n", frame, fname);
                fscanf( trajFile, "%f", &atom[0].coords[1] );
                fscanf( trajFile, "%f", &atom[0].coords[2] );
                for ( anum = 1; anum < n_atoms; anum++ ){
                        for ( c = 0; c <= 2; c++ ) fscanf( trajFile, "%f", &atom[anum].coords[c] );
                }
                writepdb(n_atoms, fname);
        }
        fclose( trajFile );
        exit( SUCCESS );
}

make_atom_table( pdb )
FILE  *pdb;
{
        int     nat;

        for ( nat=0; (fgets(line, sizeof(line), pdb)) && (nat < MAX_ATOMS); nat++ ){
                if ( (strncmp( "ATOM", line, 4 ) == 0) || (strncmp( "HETATM", line, 6 ) == 0) ){
                        sscanf(&line[ 6 ], "%d %s %s %d", &atom[ nat ].anum, atom[ nat ].aname,
                                atom[ nat ].rname, &atom[ nat ].rnum);
                }else nat--;
        }
        fclose( pdb );
        return(nat);
}

writepdb( n_atoms, fname )
int     n_atoms;
char    *fname;
{
        int     anum;
        FILE    *pdbout;

        if ( (pdbout = fopen( fname, "w")) == NULL ) {
                fprintf( stderr, "FATAL: Can't open pdb file %s\n for writing", fname );
                exit (ERROR);
        }
        for ( anum=0; anum < n_atoms; anum++ ){
                fprintf( pdbout, "ATOM %6d %-4s %3s %5d    %8.3f%8.3f%8.3f\n",
                                        atom[anum].anum, atom[anum].aname, atom[anum].rname, atom[anum].rnum,
                                        atom[anum].coords[0], atom[anum].coords[1], atom[anum].coords[2] );
        }
        return( SUCCESS );
}