[gmx-users] transfer pdb to gro
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 16 20:25:25 CEST 2008
He, Yang wrote:
> Thank you for your suggestion. I just have a doubt about the pdb file . If we need to carry on some practical problems with the gromacs, how can we get the pdb.fill .Just from the online and then make some modification based on the practical project or just write it by ourselves ? what is the use for those pdb.file online?
>
I don't know what you're asking. What modifications do you want to make? What
types of .pdb files are you thinking of using? If you're worried about
formatting issues, I've never had any problems with .pdb files from the RCSB.
I just noticed that none of your messages were sent to the gmx-users listserv;
just privately to me. Please be sure to include the users' list on all of your
messages so that others can weigh in if they have ideas as well.
-Justin
> Can you tell me that?
>
> Thank you.
>
> Yang
> ________________________________________
> From: Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Thursday, October 16, 2008 10:56 AM
> To: He, Yang; Gromacs Users' List
> Subject: Re: [gmx-users] transfer pdb to gro
>
> 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
>
> ========================================
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list