[gmx-users] pdb2gmx problem

[alexander yakovenko]

Hi All,
I have the next problem. I try to make the topology of the nonprotein molecule with 143 atoms. I found that pdb2gmx add some bonds which were not stored in rtp file, and some atoms leave separate. I check the topology manually (rtp file) and haven t fount any separated atoms in rtp. 
Why pdb2gmx add and remove some bonds automatically?
Is my molecule too large?

Thank you,

Alexander Yakovenko
Institute of Molecular Biology & Genetic of NAS of Ukraine
03143
acad.Zabolotnogo str. 150
Kiev
Ukraine
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E-mail: yakovenko_a at ukr.net