AMBER Archive (2004)

Subject: RE: AMBER: about running ptraj in amber8

From: jz7_at_duke.edu
Date: Mon Jul 26 2004 - 11:30:42 CDT

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_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
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