[gmx-users] H definition in urea topology file buildup

Divya Dube divyadube at gmail.com
Tue May 10 07:02:29 CEST 2016

Dear All,

There are four hydrogen atoms in urea molecule for which I have made H
atoms definition in aminoacids.hdb file.

URE    4
1    3    H11    N1    C    N2
1    3    H12    N1    C    N2
1    3    H21    N2    C    N1
1    3    H22    N2    C    N1

Still pdb2gmx is unable in recognizing these H atoms and giving error.
Can anyone suggest the correct way of defining urea in HDb file


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