[gmx-users] convert pdb to gro file?

David spoel at xray.bmc.uu.se
Sat Sep 27 10:24:01 CEST 2003

On Sat, 2003-09-27 at 05:34, sunzhmd at mail.ustc.edu.cn wrote:
> Hi all,
> Please help me with the pdb file that can be handled by pdb2gmx. I
> download a pdb file from a ftp server. When I used it as a input file of
> pbd2gmx, errors were encountered. I don't know why.

Please be more specific on the kind of error. 

> I here list some key words of entries of the pdb file. From the
> orgnization of the file, I think the fllowing entries is of no importance
> in creating of gromacs structure file and topology file. But can pdb2gmx
> recognize them? If no, I should remove them.
> The entries beginning with REMARK have occupied large body of the pdb
> file. Are they important? What does the number folling REMARK mean? REMARK
> 290 .....
> The rest part of the pdb file is in the attchment. It can be opened by
> notepad. As far as pdb2gmx is concerned, which entries can be recognized,
> and where should be modified?
> Thank you and regard.
> Z. H. SUN
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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