[gmx-users] ATB topology: itp to top conversion

[Anna Lappala]

Thank you Mark and Justin! That makes sense, of course!!! Many thanks.

With best wishes 
Anna

> On Jun 13, 2017, at 17:22, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> Hi,
> 
>> On Wed, Jun 14, 2017 at 1:07 AM Anna Lappala <lappala.anna at gmail.com> wrote:
>> 
>> Dear all,
>> 
>> I am confused: I have my pdb file as well as the itp file produced by ATB.
>> I want to convert these into top and gro files but the molecule is not
>> recognised by the forcefield when I do the following:
>> 
>> pdb2gmx -f input.pdb -o output.gro -i topology.itp
>> 
> 
> pdb2gmx is mostly for matching stuff found in .rtp files to produce .itp
> files. You already have your .itp file.
> 
> 
>> I have looked through tutorials and on the mailing list, but mostly the
>> workaround is to #include the itp file into an existing top file - which i
>> do not have because i only have a heteromolecule, and no protein...
>> 
> 
> The .top files are intended to be edited and written, e.g.
> 
> #include "your.ff/forcefield.itp"
> #include "heteromolecule.itp"
> #include "your.ff/spc.itp"
> [system]
> whatever name you like
> [molecules]
> hetero 1
> SOL 10123
> 
> Mark
> 
> 
>> Many thanks for any suggestions.
>> Anna
>> --
>> 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.
>> 
> -- 
> 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.