[gmx-users] How to simulate the system with 100 chains?

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Wed Oct 25 11:55:39 CEST 2006

Hi, all,
I want to simulate a unit cell of a protein under pbc. The whole system
consists of about 100 chains. In original .pdb file, some chain IDs are
identical, for example, 'A' is used for different chains. When I used
that file without revision, gmx showed error like that: Chain identifier
'A' was used in two non-sequential blocks. So I had to delete all chain
ID and hope that gmx can add them automatically accordint to its rule.
Please not that there is "TER" at the end of every  chain in my file.
But strangely, gmx did not recognize "TER" and consider some chains as
one and results in some "long bond" warning. So what can I do now?
Bacially, I maybe have two ways:
1, add different chain ID for each one, but I can't find enough
characters to do this;
2, make gmx do some help, but I can not figure out how to do till now.
Any suggestions are welcome
Zhongqiao Hu
Dept. of Chemical and Biomolecular Engineering
National Univ. of Singapore
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