[gmx-users] pdb (CTAB) into .GRO

[Tasneem Kausar]

Force field in gromacs reads only standard amino acids/DNA/RNA residue. In
your pdb file residue name XXX is not defined in gromos ff. If your system
is other than protein then use ATB to generate topolgy.

<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
Virus-free.
www.avast.com
<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Fri, Nov 3, 2017 at 2:19 PM, Adriano Santana Sanchez <
adriano.santanasanchez at kaust.edu.sa> wrote:

>  Dear all,
>
>  I am a beginner with gromacs and I have already done some online
> tutorials.
>  I am now trying to create from a PDB coordinate file (a CTAB molecule) the
>  corresponding .GRO and .TOP files to run MD simulations.
>
>  gmx pdb2gmx -f ctab.pdb -o ctab_processed.gro -water spce
>
>  then choose FF gromos96 53a6 but get error message:
>
>  Residue 'XXX' not found in topology database
>
> I am sure this FF has been used for this molecule before and I cannot
>
> find this CTAB on the residue database. What can I do?
>
> Thanks,
> Adriano
>
> --
>
> ------------------------------
> This message and its contents, including attachments are intended solely
> for the original recipient. If you are not the intended recipient or have
> received this message in error, please notify me immediately and delete
> this message from your computer system. Any unauthorized use or
> distribution is prohibited. Please consider the environment before printing
> this email.
> --
> 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.
>