He, Yang wrote:
So you have created the gro.file . I have tried your pdb.file again but it
still can not create the gro.file. It is really strange. Can you show me the
gro.file created based on the pdb.file?
The .gro I created was:
Gyas ROwers Mature At Cryogenic Speed
8
1DNA Ab 1 0.058 0.052 0.000
1DNA Tb 2 0.016 0.234 0.010
1DNA S1 3 0.236 0.657 0.120
1DNA S2 4 0.236 -0.657 -0.120
1DNA P1 5 -0.063 0.890 0.210
1DNA P2 6 -0.063 -0.890 -0.210
1DNA S3 7 -0.195 0.670 -0.460
1DNA S4 8 -0.195 -0.670 0.460
0.00000 0.00000 0.00000
When running editconf (using the .pdb I pasted below), it correctly detects 8
atoms.
-Justin
Thank you.
Yang He
________________________________________
From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Wednesday, October 15, 2008 5:27 PM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro
He, Yang wrote:
Hi Justin,
Thank you for your reply. I have followed the regular forms about pdb file but
it still shows that :
___> 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
Then you haven't followed the format correctly.
I created the following from your 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
It successfully creates a .gro file.
-Justin
So I think it is because that the atom types such as Sugar ,Adenine base are
not recognized by the gromacs .Also, what I want to solve is that how to
define these big atoms .
Do you know how to define these big atoms in order to make the gromacs
recognize them and creat the correct gro.file
Thank you .
Yang
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL
PROTECTED]
Sent: Wednesday, October 15, 2008 4:36 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] transfer pdb to gro
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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Please don't post (un)subscribe requests to the list. Use the
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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
========================================
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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