[gmx-users] problem in simulation of dna-protein complex

nitu sharma sharmanitu35 at gmail.com
Thu May 14 11:01:01 CEST 2009

Dear all ,
                I am doing simulation of DNA-protein complex.
              Is anybody have idea about  .hdb of DNA  becoz in mannual
nothing is wrritten about DNA hydrogen database .I have edited The database
like this-
ADE     9
2       6  H5*  C5*     C4*     O5*
1       5  H4*  C4*     O4*     C5*     C3*
1       5  H3*  C3*     C2*     C4*     O3*
1       5  H2*  C2*     C3*     C1*     O2`
1       2  H2`  O2`     C2*     C3*
1       5  H1*  C1*     N9      O4*     C2*
1       1  H2   C2      N1      N3
2       3  H6   N6      C6      C5
1       1  H8   C8      N9      N7

But when I run pdb2gmx command on DNA-protein pdb file the error comes like
Program pdb2gmx, VERSION 4.0.3
Source code file: h_db.c, line: 96

Fatal error:
Error in hdb file ffoplsaano.hdb:
Wrong number of control atoms (3 iso 4) on line:
1       5  H4*     C4*     O4*     C5*

If anybody have Idea what short of changes it needed please help me.
Thanks a lot in advance.

Nitu sharma
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