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

[Michael Carter]

Hi,

So adding the MODEL/ENDMDL tags worked.

However, when I now try to generate a PCA plot for this x-ray ensemble I
get a segmentation fault, as there are no eigenvectorsŠ

I used the following commands:

g_covar -s ref.pdb -f allpdb_bb.xtc


g_anaeig -s ref.pdb -f allpdb_bb.xtc -2d xray_2d.xvg -first 1 -last 2


It is after the g_anarig that the segmentation fault occurs as no
eigenvectors calculated by g_covar.

Does anyone know a solution to this problem?

Thanks
Michael




On 17/09/2014 09:25, "Tsjerk Wassenaar" <tsjerkw at gmail.com> wrote:

>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
>>
>>
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