[gmx-users] Converting multiple crystal structure PDB's into .xtc file

[Tsjerk Wassenaar]

Hi Michael,

TER is used for ending a chain. Start each pdb file with MODEL and end it
with ENDMDL. Then concatenate the pdb files and then convert.

Cheers,

Tsjerk
On Sep 17, 2014 10:22 AM, "Michael Carter" <Michael.Carter at icr.ac.uk> wrote:

> Hi,
>
> I have been trying to convert multiple PDB files into a .xtc file using
> trjconv. I have saved all the crystal structures into one large PDB (with
> TER records included). However when I perform the trjconv I obtain a .xtc
> which consists of one large co-ordinate system (80,000 atoms) rather than
> 40 representations of 2000 atoms.
>
> Therefore, once I run any further analysis, such as PCA, using a reference
> PDB file, I obtain an error where I am trying to compare a system of 2000
> atoms to the co-ordinates of a system which GROMACS thinks is 80,000 atoms
> in size.
>
> Is there a solution to writing multiple PDB's to an .xtc so that GROMACS
> understand that this is a crystal structure trajectory rather than one
> large system?
>
> Thanks,
> Michael
>
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No.
> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee only.  If
> the message is received by anyone other than the addressee, please return
> the message to the sender by replying to it and then delete the message
> from your computer and network.
> --
> 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.
>