Dear Users,
I would like to convert my psf/pdb file generated by VMD (psfgen) to
amber style format.
Unfortunately, I obtained the following error:
At line 2690 of file _psfprm.f (unit = 20, file = 'my.psf')
Fortran runtime error: Bad value during integer read.
I used the ala_ala_ala.pdb file as input (test/chamber/ala_ala_ala), and
the psf/pdb file was generated by VMD/psfgen, and i obtained the same error.
How can I sole this problem?
The obtained output files are attached:
ala_ala_ala.pdb.BAK & ala_ala_ala.psf.BAK - original pdb and psf file
from amber dsitribution
ala_ala_ala.pdb & ala_ala_ala.psf - generated by VMD/psfgen
Thank you for your help in advance!
Balazs
PSF CMAP
6 !NTITLE
REMARKS original generated structure x-plor psf file
REMARKS 2 patches were applied to the molecule.
REMARKS topology ala_ala_ala_autopsf-temp.top
REMARKS segment P1 { first NTER; last CTER; auto angles dihedrals }
REMARKS patch NTER P1:1
REMARKS patch CTER P1:3
33 !NATOM
1 P1 1 ALA N NH3 -0.300000 14.0070 0
2 P1 1 ALA HT1 HC 0.330000 1.0080 0
3 P1 1 ALA HT2 HC 0.330000 1.0080 0
4 P1 1 ALA HT3 HC 0.330000 1.0080 0
5 P1 1 ALA CA CT1 0.210000 12.0110 0
6 P1 1 ALA HA HB 0.100000 1.0080 0
7 P1 1 ALA CB CT3 -0.270000 12.0110 0
8 P1 1 ALA HB1 HA 0.090000 1.0080 0
9 P1 1 ALA HB2 HA 0.090000 1.0080 0
10 P1 1 ALA HB3 HA 0.090000 1.0080 0
11 P1 1 ALA C C 0.510000 12.0110 0
12 P1 1 ALA O O -0.510000 15.9990 0
13 P1 2 ALA N NH1 -0.470000 14.0070 0
14 P1 2 ALA HN H 0.310000 1.0080 0
15 P1 2 ALA CA CT1 0.070000 12.0110 0
16 P1 2 ALA HA HB 0.090000 1.0080 0
17 P1 2 ALA CB CT3 -0.270000 12.0110 0
18 P1 2 ALA HB1 HA 0.090000 1.0080 0
19 P1 2 ALA HB2 HA 0.090000 1.0080 0
20 P1 2 ALA HB3 HA 0.090000 1.0080 0
21 P1 2 ALA C C 0.510000 12.0110 0
22 P1 2 ALA O O -0.510000 15.9990 0
23 P1 3 ALA C CC 0.340000 12.0110 0
24 P1 3 ALA OT1 OC -0.670000 15.9990 0
25 P1 3 ALA OT2 OC -0.670000 15.9990 0
26 P1 3 ALA N NH1 -0.470000 14.0070 0
27 P1 3 ALA HN H 0.310000 1.0080 0
28 P1 3 ALA CA CT1 0.070000 12.0110 0
29 P1 3 ALA HA HB 0.090000 1.0080 0
30 P1 3 ALA CB CT3 -0.270000 12.0110 0
31 P1 3 ALA HB1 HA 0.090000 1.0080 0
32 P1 3 ALA HB2 HA 0.090000 1.0080 0
33 P1 3 ALA HB3 HA 0.090000 1.0080 0
32 !NBOND: bonds
1 5 2 1 3 1 4 1
5 6 7 5 7 8 7 9
7 10 11 5 11 13 12 11
13 14 13 15 15 16 17 15
17 18 17 19 17 20 21 15
21 26 22 21 23 25 23 24
23 28 26 27 26 28 28 29
30 28 30 31 30 32 30 33
57 !NTHETA: angles
1 5 6 1 5 11 2 1 5
2 1 4 2 1 3 3 1 5
3 1 4 4 1 5 5 11 12
5 11 13 5 7 10 5 7 9
5 7 8 7 5 6 7 5 11
7 5 1 8 7 10 8 7 9
9 7 10 11 5 6 13 15 16
13 15 21 13 11 12 14 13 11
14 13 15 15 21 22 15 21 26
15 17 20 15 17 19 15 17 18
15 13 11 17 15 16 17 15 21
17 15 13 18 17 20 18 17 19
19 17 20 21 15 16 23 28 29
24 23 28 25 23 28 25 23 24
26 28 29 26 28 23 26 21 22
27 26 21 27 26 28 28 30 33
28 30 32 28 30 31 28 26 21
30 28 29 30 28 23 30 28 26
31 30 33 31 30 32 32 30 33
74 !NPHI: dihedrals
1 5 7 8 1 5 7 9
1 5 7 10 1 5 11 13
1 5 11 12 2 1 5 7
2 1 5 11 2 1 5 6
3 1 5 7 3 1 5 11
3 1 5 6 4 1 5 7
4 1 5 11 4 1 5 6
5 11 13 14 5 11 13 15
6 5 7 8 6 5 7 9
6 5 7 10 6 5 11 13
6 5 11 12 7 5 11 13
7 5 11 12 8 7 5 11
9 7 5 11 10 7 5 11
11 13 15 17 11 13 15 21
11 13 15 16 12 11 13 14
12 11 13 15 13 15 17 18
13 15 17 19 13 15 17 20
13 15 21 26 13 15 21 22
14 13 15 17 14 13 15 21
14 13 15 16 15 21 26 27
15 21 26 28 16 15 17 18
16 15 17 19 16 15 17 20
16 15 21 26 16 15 21 22
17 15 21 26 17 15 21 22
18 17 15 21 19 17 15 21
20 17 15 21 21 26 28 30
21 26 28 23 21 26 28 29
22 21 26 27 22 21 26 28
23 28 30 31 23 28 30 32
23 28 30 33 23 28 26 27
24 23 28 30 24 23 28 26
24 23 28 29 25 23 28 30
25 23 28 26 25 23 28 29
26 28 30 31 26 28 30 32
26 28 30 33 27 26 28 30
27 26 28 29 29 28 30 31
29 28 30 32 29 28 30 33
5 !NIMPHI: impropers
11 5 13 12 13 11 15 14
21 15 26 22 23 28 25 24
26 21 28 27
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0
1 0 !NGRP
0 0 0
1 !NCRTERM: cross-terms
11 13 15 21 13 15 21 26
At line 2690 of file _psfprm.f (unit = 20, file = 'ala_ala_ala.psf')
Fortran runtime error: Bad value during integer read
| *****************************************************
| * CHAMBER: Charmm psf to AMBER prmtop convertor *
| * *
| * v1.0 *
| * *
| * Written by: *
| * Mark J. Williamson *
| * Michael F. Crowley *
| * Ross C. Walker *
| * *
| *****************************************************
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Received on Thu Feb 18 2010 - 14:00:06 PST
