[gmx-users] Re: getting a good .gro file from a pdb file while thetopology is ready

[Allen Smith]

In message <1191454900.470428b4c19a5 at webmail.vt.edu> (on 3 October 2007
19:41:40 -0400), jalemkul at vt.edu (Justin A. Lemkul) wrote:
>You can use editconf to directly convert a .pdb file into .gro format.

Good point.

>-Justin
>
>Quoting maria goranovic <mariagoranovic at gmail.com>:
>
>>  Thank you all for the replies and help.

Quite welcome; hope my reply was at least slightly helpful...

>> The main reason I was messing with
>> pdb2gmx, editconf and genbox was mainly to convert my pdb into a nice .gro
>> format file, which I could input into grompp. I understand grompp can take a
>> pdb file for input as well. Does it not need any "box" information, like the
>> box type, or the dimensions ? If it can infer these directly from the pdb,
>> or these details can be specified in the .mdp file then my problems are
>> solved.

With regard to the box, that you are dealing with a planar system might,
again, make a difference here; this is not my area, however.

       -Allen

>> I will look more carefully into the -h ..
>>
>> Thank you !
>>
>> -Maria
>>
>>
>> Message: 6
>> > Date: Thu, 04 Oct 2007 03:51:27 +1000
>> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> > Subject: Re: [gmx-users] getting a good .gro file from a pdb file
>> >        while the       topology is ready
>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> > Message-ID: <4703D69F.5000005 at anu.edu.au>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> >
>> > Hydrogen takes up volume too... your equilibration will be less
>> > troublesome if your whole system "fits" at the start of the equilibration.
>> >
>> > It sounds like it might be worth your while reading the introductory
>> > part of pdb2gmx -h, editconf -h, genbox -h, etc. so you have an idea
>> > what each tool is trying to do. Following a recipe without appreciating
>> > what you're doing is fine, until you go to change the recipe, which is
>> > what you're trying to do here. :-)
>> >
>> > Mark
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 7
>> > Date: Thu, 04 Oct 2007 04:04:05 +1000
>> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> > Subject: Re: [gmx-users] getting a good .gro file from a pdb file
>> >        while the       topology is ready
>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> > Message-ID: <4703D995.40608 at anu.edu.au>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> > Allen Smith wrote:
>> > > In message <9024f1330710031013t10772b86nfb62129ec625c03e at mail.gmail.com>
>> > (on
>> > > 3 October 2007 19:13:51 +0200), mariagoranovic at gmail.com (maria
>> > goranovic)
>> > > wrote:
>> > >> Hi,
>> > >>
>> > >> I had a large bilayer in .gro and .top gromacs format files
>> > >
>> > > Bilayer? I believe there are some specific things for doing planar
>> > periodic
>> > > boundary conditions (or planar infinite system conditions), but I am not
>> > > familiar with them.
>> >
>> > Yeah but they're in the .mdp and not the issue here :-)


-- 
Allen Smith                       http://cesario.rutgers.edu/easmith/
February 1, 2003                               Space Shuttle Columbia
Ad Astra Per Aspera                     To The Stars Through Asperity