Thanks for the reply. Here is my psf file. It's very long, so I'll just
paste the beginning part.
The following is the psf file I am using:
PSF
1 !NTITLE
REMARKS original generated structure x-plor psf file
60787 !NATOM
1 PRO1 1 ALA N NH3 -0.300000 14.0070 0
2 PRO1 1 ALA HT1 HC 0.330000 1.0080 0
3 PRO1 1 ALA HT2 HC 0.330000 1.0080 0
4 PRO1 1 ALA HT3 HC 0.330000 1.0080 0
5 PRO1 1 ALA CA CT1 0.210000 12.0110 0
6 PRO1 1 ALA HA HB 0.100000 1.0080 0
7 PRO1 1 ALA CB CT3 -0.270000 12.0110 0
8 PRO1 1 ALA HB1 HA 0.090000 1.0080 0
9 PRO1 1 ALA HB2 HA 0.090000 1.0080 0
10 PRO1 1 ALA HB3 HA 0.090000 1.0080 0
11 PRO1 1 ALA C C 0.510000 12.0110 0
12 PRO1 1 ALA O O -0.510000 15.9990 0
13 PRO1 2 GLU N NH1 -0.470000 14.0070 0
14 PRO1 2 GLU HN H 0.310000 1.0080 0
15 PRO1 2 GLU CA CT1 0.070000 12.0110 0
16 PRO1 2 GLU HA HB 0.090000 1.0080 0
17 PRO1 2 GLU CB CT2 -0.180000 12.0110 0
18 PRO1 2 GLU HB1 HA 0.090000 1.0080 0
19 PRO1 2 GLU HB2 HA 0.090000 1.0080 0
20 PRO1 2 GLU CG CT2 -0.280000 12.0110 0
21 PRO1 2 GLU HG1 HA 0.090000 1.0080 0
22 PRO1 2 GLU HG2 HA 0.090000 1.0080 0
23 PRO1 2 GLU CD CC 0.620000 12.0110 0
24 PRO1 2 GLU OE1 OC -0.760000 15.9990 0
25 PRO1 2 GLU OE2 OC -0.760000 15.9990 0
26 PRO1 2 GLU C C 0.510000 12.0110 0
27 PRO1 2 GLU O O -0.510000 15.9990 0
28 PRO1 3 TRP N NH1 -0.470000 14.0070 0
29 PRO1 3 TRP HN H 0.310000 1.0080 0
30 PRO1 3 TRP CA CT1 0.070000 12.0110 0
31 PRO1 3 TRP HA HB 0.090000 1.0080 0
32 PRO1 3 TRP CB CT2 -0.180000 12.0110 0
33 PRO1 3 TRP HB1 HA 0.090000 1.0080 0
34 PRO1 3 TRP HB2 HA 0.090000 1.0080 0
35 PRO1 3 TRP CG CY -0.030000 12.0110 0
36 PRO1 3 TRP CD1 CA 0.035000 12.0110 0
37 PRO1 3 TRP HD1 HP 0.115000 1.0080 0
38 PRO1 3 TRP NE1 NY -0.610000 14.0070 0
39 PRO1 3 TRP HE1 H 0.380000 1.0080 0
40 PRO1 3 TRP CE2 CPT 0.130000 12.0110 0
41 PRO1 3 TRP CD2 CPT -0.020000 12.0110 0
42 PRO1 3 TRP CE3 CA -0.115000 12.0110 0
43 PRO1 3 TRP HE3 HP 0.115000 1.0080 0
44 PRO1 3 TRP CZ3 CA -0.115000 12.0110 0
45 PRO1 3 TRP HZ3 HP 0.115000 1.0080 0
46 PRO1 3 TRP CZ2 CA -0.115000 12.0110 0
47 PRO1 3 TRP HZ2 HP 0.115000 1.0080 0
48 PRO1 3 TRP CH2 CA -0.115000 12.0110 0
49 PRO1 3 TRP HH2 HP 0.115000 1.0080 0
50 PRO1 3 TRP C C 0.510000 12.0110 0
51 PRO1 3 TRP O O -0.510000 15.9990 0
52 PRO1 4 SER N NH1 -0.470000 14.0070 0
53 PRO1 4 SER HN H 0.310000 1.0080 0
54 PRO1 4 SER CA CT1 0.070000 12.0110 0
55 PRO1 4 SER HA HB 0.090000 1.0080 0
56 PRO1 4 SER CB CT2 0.050000 12.0110 0
57 PRO1 4 SER HB1 HA 0.090000 1.0080 0
58 PRO1 4 SER HB2 HA 0.090000 1.0080 0
59 PRO1 4 SER OG OH1 -0.660000 15.9990 0
60 PRO1 4 SER HG1 H 0.430000 1.0080 0
61 PRO1 4 SER C C 0.510000 12.0110 0
62 PRO1 4 SER O O -0.510000 15.9990 0
63 PRO1 5 GLY N NH1 -0.470000 14.0070 0
64 PRO1 5 GLY HN H 0.310000 1.0080 0
65 PRO1 5 GLY CA CT2 -0.020000 12.0110 0
66 PRO1 5 GLY HA1 HB 0.090000 1.0080 0
67 PRO1 5 GLY HA2 HB 0.090000 1.0080 0
68 PRO1 5 GLY C C 0.510000 12.0110 0
69 PRO1 5 GLY O O -0.510000 15.9990 0
70 PRO1 6 GLU N NH1 -0.470000 14.0070 0
71 PRO1 6 GLU HN H 0.310000 1.0080 0
72 PRO1 6 GLU CA CT1 0.070000 12.0110 0
73 PRO1 6 GLU HA HB 0.090000 1.0080 0
74 PRO1 6 GLU CB CT2 -0.180000 12.0110 0
75 PRO1 6 GLU HB1 HA 0.090000 1.0080 0
76 PRO1 6 GLU HB2 HA 0.090000 1.0080 0
77 PRO1 6 GLU CG CT2 -0.280000 12.0110 0
78 PRO1 6 GLU HG1 HA 0.090000 1.0080 0
79 PRO1 6 GLU HG2 HA 0.090000 1.0080 0
80 PRO1 6 GLU CD CC 0.620000 12.0110 0
81 PRO1 6 GLU OE1 OC -0.760000 15.9990 0
82 PRO1 6 GLU OE2 OC -0.760000 15.9990 0
83 PRO1 6 GLU C C 0.510000 12.0110 0
84 PRO1 6 GLU O O -0.510000 15.9990 0
85 PRO1 7 TYR N NH1 -0.470000 14.0070 0
86 PRO1 7 TYR HN H 0.310000 1.0080 0
87 PRO1 7 TYR CA CT1 0.070000 12.0110 0
88 PRO1 7 TYR HA HB 0.090000 1.0080 0
89 PRO1 7 TYR CB CT2 -0.180000 12.0110 0
90 PRO1 7 TYR HB1 HA 0.090000 1.0080 0
91 PRO1 7 TYR HB2 HA 0.090000 1.0080 0
92 PRO1 7 TYR CG CA 0.000000 12.0110 0
93 PRO1 7 TYR CD1 CA -0.115000 12.0110 0
94 PRO1 7 TYR HD1 HP 0.115000 1.0080 0
95 PRO1 7 TYR CE1 CA -0.115000 12.0110 0
96 PRO1 7 TYR HE1 HP 0.115000 1.0080 0
97 PRO1 7 TYR CZ CA 0.110000 12.0110 0
98 PRO1 7 TYR OH OH1 -0.540000 15.9990 0
99 PRO1 7 TYR HH H 0.430000 1.0080 0
100 PRO1 7 TYR CD2 CA -0.115000 12.0110 0
101 PRO1 7 TYR HD2 HP 0.115000 1.0080 0
102 PRO1 7 TYR CE2 CA -0.115000 12.0110 0
103 PRO1 7 TYR HE2 HP 0.115000 1.0080 0
104 PRO1 7 TYR C C 0.510000 12.0110 0
105 PRO1 7 TYR O O -0.510000 15.9990 0
106 PRO1 8 ILE N NH1 -0.470000 14.0070 0
107 PRO1 8 ILE HN H 0.310000 1.0080 0
108 PRO1 8 ILE CA CT1 0.070000 12.0110 0
109 PRO1 8 ILE HA HB 0.090000 1.0080 0
110 PRO1 8 ILE CB CT1 -0.090000 12.0110 0
111 PRO1 8 ILE HB HA 0.090000 1.0080 0
112 PRO1 8 ILE CG2 CT3 -0.270000 12.0110 0
113 PRO1 8 ILE HG21 HA 0.090000 1.0080 0
114 PRO1 8 ILE HG22 HA 0.090000 1.0080 0
115 PRO1 8 ILE HG23 HA 0.090000 1.0080 0
116 PRO1 8 ILE CG1 CT2 -0.180000 12.0110 0
117 PRO1 8 ILE HG11 HA 0.090000 1.0080 0
118 PRO1 8 ILE HG12 HA 0.090000 1.0080 0
119 PRO1 8 ILE CD CT3 -0.270000 12.0110 0
120 PRO1 8 ILE HD1 HA 0.090000 1.0080 0
121 PRO1 8 ILE HD2 HA 0.090000 1.0080 0
122 PRO1 8 ILE HD3 HA 0.090000 1.0080 0
123 PRO1 8 ILE C C 0.510000 12.0110 0
124 PRO1 8 ILE O O -0.510000 15.9990 0
125 PRO1 9 SER N NH1 -0.470000 14.0070 0
126 PRO1 9 SER HN H 0.310000 1.0080 0
127 PRO1 9 SER CA CT1 0.070000 12.0110 0
128 PRO1 9 SER HA HB 0.090000 1.0080 0
129 PRO1 9 SER CB CT2 0.050000 12.0110 0
130 PRO1 9 SER HB1 HA 0.090000 1.0080 0
131 PRO1 9 SER HB2 HA 0.090000 1.0080 0
132 PRO1 9 SER OG OH1 -0.660000 15.9990 0
133 PRO1 9 SER HG1 H 0.430000 1.0080 0
134 PRO1 9 SER C C 0.510000 12.0110 0
135 PRO1 9 SER O O -0.510000 15.9990 0
136 PRO1 10 PRO N N -0.290000 14.0070 0
137 PRO1 10 PRO CD CP3 0.000000 12.0110 0
138 PRO1 10 PRO HD1 HA 0.090000 1.0080 0
139 PRO1 10 PRO HD2 HA 0.090000 1.0080 0
140 PRO1 10 PRO CA CP1 0.020000 12.0110 0
141 PRO1 10 PRO HA HB 0.090000 1.0080 0
142 PRO1 10 PRO CB CP2 -0.180000 12.0110 0
143 PRO1 10 PRO HB1 HA 0.090000 1.0080 0
144 PRO1 10 PRO HB2 HA 0.090000 1.0080 0
145 PRO1 10 PRO CG CP2 -0.180000 12.0110 0
146 PRO1 10 PRO HG1 HA 0.090000 1.0080 0
147 PRO1 10 PRO HG2 HA 0.090000 1.0080 0
148 PRO1 10 PRO C C 0.510000 12.0110 0
149 PRO1 10 PRO O O -0.510000 15.9990 0
150 PRO1 11 TYR N NH1 -0.470000 14.0070 0
151 PRO1 11 TYR HN H 0.310000 1.0080 0
......
On Mon, 26 Jul 2004, Ross Walker wrote:
>
> > I was trying to run ptraj in Amber8. But it has problem to read Charmm
> > format file (topology psf file). I am wondering if there is any defaut
> > Amber format setting? I tried it on the old ptraj version
> > (seperated from
> > Amber), it worked. Any idea why this happened?
>
> Can you post your psf file please. There is no obvious difference between
> amber8 ptraj.c and amber7 ptraj.c that involves the decision on whether a
> file is an Amber or Charmm topology file. The code that decides is:
>
> if (strcmp(buffer, "PSF \n") == 0)
> state = loadCharmmPSF(fp, 1);
> else {
> safe_freopen(fp);
>
> So quickly check the first line of your charmm topology file and see if
> contains the string "PSF ".
>
> If you can post me the psf file I can look deeper.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Jul 26 2004 - 17:53:00 PDT
