He, Yang wrote:
the operating system is unix and the version is about 3.1.1. I have no idea
whether this will influence the result.
Version 3.1.1 is very old; upgrade to a newer version and try again.
-Justin
It always 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 hao.pdb is 0
Read 0 atoms
Volume: 0 nm^3, corresponds to roughly 0 electrons
No velocities found
My created file is : Gromacs Runs One Microsecond At Cannonball Speeds
0
2.00000 2.00000 2.00000
no atoms included
Thank you
Yang
________________________________________
From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Thursday, October 16, 2008 10:47 AM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro
He, Yang wrote:
Hi Justin.
I just followed the pdb file from you but I can still not create the correct
gro.file. I use this command editconf -f hao.pdb -o hao.gro -d 1.0
What is the problem . And I find what you create for the pdb file based on mine
almost makes no difference .
I have no idea what the problem is. What's in the .gro file?
Sometimes tools don't function properly when they haven't been installed
correctly. What is your operating system? What version of Gromacs are you
using? What were the compilers (and versions)? Did the installation process
report any errors?
-Justin
Thank you for your guidance.
Yang He
________________________________________
From: Justin A. Lemkul [EMAIL PROTECTED]
Sent: Wednesday, October 15, 2008 5:48 PM
To: He, Yang; Gromacs Users' List
Subject: Re: [gmx-users] transfer pdb to gro
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
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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
========================================
--
========================================
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 gmx-users@gromacs.org
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
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
