AMBER: Amber: Anal program format

From: Helios <p9890101.mail.ncku.edu.tw>
Date: Tue, 17 Aug 2004 14:15:57 +0800

Dear all, I am trying to run amber7/test/vac_rna example, and I found the
format of prmtop file in vac_rna folder is different from the prmtop
generated by xleap. So there is an error message " FATAL: Topology and
coord files do not match" when I run anal program. Is there any method to
transform these two format or any method to solve it? The following is two
files format I extracted:

prmtop (amber7/test/vac_rna)

PDB 5DNB, Dickerson decamer
  640 15 220 468 500 726 918 1030 0 0 3568 20
  468 726 1030 49 112 70 24 0 0 0 0 0
    0 0 0 0 35 0
H5T O5' C5' H5'1H5'2C4' H4' O4' C1' H1' N1 C6 H6 C5 H5 C4 N4 H41 H42
N3
C2 O2 C3' H3' C2' H2'1O2' HO'2O3' P O1P O2P O5' C5' H5'1H5'2C4' H4' O4'
C1'
H1' N1 C6 H6 C5 H5 C4 N4 H41 H42 N3 C2 O2 C3' H3' C2' H2'1O2'
HO'2O3'

another prmtop(generate by xleap's saveamberparm command)
%FORMAT
(20a4)
                                                                              
%FLAG
POINTERS
%FORMAT
(10I8)
    547 17 345 226 268 347 518 613
0 0
   2062 87 226 347 613 39 76 42
27 1
      0 0 0 0 0 0 0 0
34 0
      0
%FLAG
ATOM_NAME
%FORMAT
(20a4)
H5T O5' C5' H5'1H5'2C4' H4' O4' C1' H1' N1 C6 H6 C5 H5 C4 N4 H41 H42
N3
C2 O2 C3' H3' C2' H2'1H2'2O3' P O1P O2P O5' C5' H5'1H5'2C4' H4' O4' C1'
H1'
N1 C6 H6 C5 H5 C4 N4 H41 H42 N3 C2 O2 C3' H3' C2' H2'1H2'2O3' P
O1P


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Received on Tue Aug 17 2004 - 07:53:02 PDT
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