nitu sharma wrote:
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 this-
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.
The hydrogen database format is described in chapter 5. The description
is not a work of art, but you should start looking there.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
