[gmx-users] Problem on processing proteins consisting of two chains

[wang chuanming]

Dear all,
  I am a new user of Gromacs.I am trying to do a simulation on a protein 
which consists of two chains(A and B) like HIV PR.Unfortunately, the two 
chains got far away from each other. I found that two itp 
files(protein_A.itp and protein_B.itp) were generated after using pdb2gmx. 
It seems that Gromacs recognizes the two chains as different proteins,but 
they belong to the same molecule indeed. 
  How can I resolve the problem? Your experiences on Gromacs will helful 
for me.

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