[gmx-users] transfer pdb to gro
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 16 19:56:54 CEST 2008
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 [jalemkul at vt.edu]
> 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 [jalemkul at vt.edu]
>> 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 [jalemkul at vt.edu]
>>> 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: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
>>>> 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
>>>>> _______________________________________________
>>>>> gmx-users mailing list gmx-users at 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 gmx-users-request at gromacs.org.
>>>>> 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
>>>>
>>>> ========================================
>>>> _______________________________________________
>>>> gmx-users mailing list gmx-users at 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 gmx-users-request at gromacs.org.
>>>> 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
========================================
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