AMBER Archive (2009)

Subject: [AMBER] xleap reading hydrogens giving error

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Fri May 15 2009 - 02:47:10 CDT

Hi all,

I am using vmd visualize my md simulation if I save a pdb file from vmd and
want to build parameter file or just load it into xleap it cannot read the
hydrogens as VMD is saving it differently from what xleap wants to read :

ATOM 1 N GLN 1 39.739 -9.379 23.270 1.00
1.00
ATOM 2 H1 GLN 1 39.228 -10.233 23.088 1.00
0.00
ATOM 3 H2 GLN 1 40.696 -9.602 23.511 1.00
0.00
ATOM 4 H3 GLN 1 39.297 -8.892 24.035 1.00
0.00
ATOM 5 CA GLN 1 39.723 -8.542 22.049 1.00
1.00
ATOM 6 HA GLN 1 38.688 -8.313 21.792 1.00
0.00
ATOM 7 CB GLN 1 40.460 -7.222 22.241 1.00
1.00
ATOM 8 2HB GLN 1 41.513 -7.459 22.401 1.00
0.00
ATOM 9 3HB GLN 1 40.425 -6.562 21.370 1.00
0.00

ATOM 1 N GLN 1 39.739 -9.379 23.270 1.00 0.00
ATOM 2 H1 GLN 1 39.228 -10.233 23.088 1.00 0.00
ATOM 3 H2 GLN 1 40.696 -9.602 23.511 1.00 0.00
ATOM 4 H3 GLN 1 39.297 -8.892 24.035 1.00 0.00
ATOM 5 CA GLN 1 39.723 -8.542 22.049 1.00 0.00
ATOM 6 HA GLN 1 38.688 -8.313 21.792 1.00 0.00
ATOM 7 CB GLN 1 40.460 -7.222 22.241 1.00 0.00
ATOM 8 2HB GLN 1 41.535 -7.381 22.326 1.00 0.00
ATOM 9 3HB GLN 1 40.259 -6.537 21.418 1.00 0.00

so it will give an error reading 2HB and then add another 2HB - is there a
simple command in xleap fix this?

Thanks in advance

Best
Jorgen
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