[gmx-users] topology for large molecule

Hideki Takehara take at grt.kyushu-u.ac.jp
Thu Nov 15 11:25:23 CET 2001

Hello everyone,

    I want to do MD simulation of a protein including sugar polymers.  I
believe the gromacs is very sophisticate system to do so. but  I am a
beginner for using gromacs, so please anybody help me. my questions are
1. How to create topology of large molecules. At first, I was attempt to
do with PRODRG server, but it said my molecule is too large to create
topology. My molecule is hexa-GlcNAc(N-acetyl glucosamin) which has 85
atoms without hydrogen. PRODRG said it is impossible because of
limitation of gromacs topolgy discription.
2. How to define connectivity between monomers. Next, I tried to create
a topolgy file for monomer and
connect them like amino acid chain. But I can not find files or data
about this. I guess I can add GlcNAc to aminoacid.dat file like the case
of a modified  amino acid. but I am wondering how to treate gycosil
    I guess this might be FAQ??
    Please give me your help. Thanks in advance.

Hideki Takehara  take at grt.kyushu-u.ac.jp
Molecular Gene Technics, Genetic Resource Technology,
          Kyushu University
              Tel +81-92-642-3041 Fax +81-92-642-3043

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