[gmx-users] GMX-compatible DNA coordinates

[Mark Abraham]

On 03/04/2015 5:53 pm, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>
> Hi,
>
> I tried that search myself and found some things that looked potentially
useful to you, so I suggested that search. Either you might find something
useful there, or the dialogue could progress about what you need. Requiring
perfect input for pdb2gmx is a fairly stringent expectation.

i.e. The use of sed or similar tools is normal, as Tsjerk says also. There
are too many options, and nobody has built the Babel fish of MD input!

Mark

> Mark
>
> On 03/04/2015 3:40 pm, "Alex" <nedomacho at gmail.com> wrote:
>>
>> Mark,
>>
>>
>> Not to troll, but why did you assume that I didn't do my due diligence
before posting here?
>>
>> Because, you see, you could have left that second part of your reply
(which only confirms the legitimacy of my initial question), and it would
make it less insulting.
>>
>>
>> Alex
>>
>>
>>
>> >
>>
>> Hi,
>>
>> Googling things like "gromacs DNA structure" is a good bet. There are no
fully standardised naming schemes or workflows, so you will likely not have
something do everything for you.
>>
>> Mark
>>
>> On 03/04/2015 7:03 am, "Alex" <nedomacho at gmail.com> wrote:
>>
>>
>> I'm fully aware that this is a forum for discussing Gromacs, but there's
a bit of a frustrating situation that involves using it.
>>
>> I need a linear ssDNA chain, sequence of my choosing, anything that will
work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields
for it, everything as is. You suggested AMBER in the past, so AMBER it is.
>>
>>
>> ChemOffice produced a PDB with incompatible atom types. make-na server (
http://structure.usc.edu/make-na/server.html) also produced something
pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a
usable topology out of the box with an established potential implemented in
Gromacs? Anything that will not involve manual modification of PDBs or
writing text-processing scripts will make me very happy.
>>
>>
>> I will really appreciate any suggestions.
>>
>>
>> Thank you,
>>
>>
>> Alex
>>
>>
>>
>>
>> --
>>
>> Gromacs Users mailing list
>>
>>
>> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>> * For (un)subscribe requests visit
>>
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-request at gromacs.org.
>>
>>
>>
>>
>>
>> --
>>
>> Best regards,
>>
>>  Alex                            mailto:nedomacho at gmail.com
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-request at gromacs.org.