[gmx-users] missing residues

Yu Sun (Denis) sun at CLEMSON.EDU
Wed Mar 17 18:17:00 CET 2004

Dear gmx-users,

I am dealing with a large protein (~ 75kD). There are some missing
residues and atoms. For example, there are 9 residues missing in sequence ( 
21 to 29 ). I used InsightII to add all the missing residues and atoms.
Then I am trying to use Gromacs to do energy minimization. But I got  fmax =
inf  and energy is very high( positive 10^5).

I took out residues from 20 to 30  to obtain a pdb file with 11
residues and fixed  residue 20 and 30 to do energy minimization (in vacuum),
still got very high positive energy. When not fixing 20 and 30, negative
energy can be obtained ( negative 10^3).

Can anyone suggest me how to deal with such problems, i.e. add
missing  disordered residues in a pdb file and get reasonable structure?


Yu Sun

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