Dear all ,<br> I am doing simulation of DNA-protein complex.<br> 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-<br>
ADE 9<br>2 6 H5* C5* C4* O5*<br>1 5 H4* C4* O4* C5* C3*<br>1 5 H3* C3* C2* C4* O3*<br>1 5 H2* C2* C3* C1* O2`<br>1 2 H2` O2` C2* C3*<br>
1 5 H1* C1* N9 O4* C2*<br>1 1 H2 C2 N1 N3<br>2 3 H6 N6 C6 C5<br>1 1 H8 C8 N9 N7<br><br>But when I run pdb2gmx command on DNA-protein pdb file the error comes like this-<br>
Program pdb2gmx, VERSION 4.0.3<br>Source code file: h_db.c, line: 96<br><br>Fatal error:<br>Error in hdb file ffoplsaano.hdb:<br>Wrong number of control atoms (3 iso 4) on line:<br>1 5 H4* C4* O4* C5* <br>
<br>If anybody have Idea what short of changes it needed please help me.<br>Thanks a lot in advance.<br><br>Nitu sharma<br><br>