He, Yang wrote:
Hi all users,
When I use the editconf command to transform pdb file to gro file, it shows
like this
Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Warning: Number of atoms in atom.pdb is 0
WARNING: all CONECT records are ignored
Read 0 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found
And this is my original pdb file
ATOM 1 Ab DNA 0.575 0.516 0.051 1.0 0.0
ATOM 2 Tb DNA 0.159 2.344 0.191 1.0 0.0
ATOM 3 S1 DNA 2.365 6.568 1.280 1.0 0.0
ATOM 4 S2 DNA 2.365 -6.568 -1.280 1.0 0.0
ATOM 5 P1 DNA -0.628 8.896 2.186 1.0 0.0
ATOM 6 P2 DNA -0.628 -8.896 -2.186 1.0 0.0
ATOM 7 S3 DNA -1.947 6.704 -4.660 1.0 0.0
ATOM 8 S4 DNA -1.947 -6.704 4.660 1.0 0.0
CONECT 1 3
CONECT 2 4
CONECT 3 1 5
CONECT 4 2 6
CONECT 5 3 7
CONECT 6 4 8
CONECT 7 5
CONECT 8 6
MASTER 0 0 0 0 0 0 0 0 8 0 8 0
END
not very complex, only 8 atoms . And I find these atoms are not included in
the gromacs so i defined them in the .atp file this
Ab 134.1; Adenine base of DNA
Tb 125.1; Thymine base of DNA
S 83.11; Sugar of DNA
P 94.97; Phosphate of DNA
The .atp file means nothing for editconf.
Can anyone of you help me sovle this problem?
It looks like the formatting of your .pdb file is irregular. A fixed format is
required for proper detection of atoms and coordinates. See here:
http://www.wwpdb.org/docs.html
-Justin
Thank you in advance
Yang He
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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