[gmx-users] How to create top of small molecules with pdb2gmx

Tingguang.S tingguang.sun at gxust.edu.cn
Thu Mar 28 14:15:24 CET 2019

Dear all,

      I am trying to create the topology of a system with 100 formic acid molecules in the box. Charmm36 force filed was used, and I noticed that the corresponding entry for formic acid in this force filed was residue FORH. When I typed the command line: gmx pdb2gmx -f formic-acid.pdb, the error code is: "Atom HN in residue FORH 1 was not found in rtp entry FORH with 5 atoms". It seems that pdb2gmx automatically added the N terminus. How can I avoid this auto addition of the terminus. If pdb2gmx can not be used to generate a small molecule top file, then how can I make use of the parameters which had been defined in the existed force filed files (In this case, the residue FORH).

    Thank you for your time !

    Best regards

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