[gmx-users] [Fwd: help me please]

[sunzhmd at mail.ustc.edu.cn]

Hi all,

I download a pdb file of DEOXYRIBONUCLEIC ACID with many records.Then I
want to convert it into a gromacs structure file .gro by the
command

pdb2gmx -f filename.pdb

Then a error was encountered which reads

Residue 'A' not found in residue topology file database

I do not know why. I wonder if you can do me a favor and help me with this
question.

By the way, I am a new guy to gromacs. So I wonder if you can tell me
which records are useful in a officially distributed standard pdb file, as
far as md simulation is concerned. Are there any differences in format
between a pdb file that can be handled by pdb2gmx and a officially
distributed standard pdb file.

Or if you can give me a example pdb file used by gromacs with all possible
usefull record names and formats.

The file I download is attached here. If you have time, I beg you to help
me check it to see why such error was encountered.

Thank you very much and best regards.

Zehui Sun


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