Hi,
The 'remap' command in cpptraj can be used to re-order atoms according
to an input data file. So if e.g. you have 9 atoms and you want to
switch atoms 4-6 with atoms 7-9 you would have a file like:
1 1
2 2
3 3
4 7
5 8
6 9
7 4
8 5
9 6
then do something like
parm MyParm.parm7
trajin MyTraj.nc
readdata remap.dat name MyData
remap data MyData parmout Remap.parm7
trajout remap.nc
Hope this helps,
-Dan
On Sun, Sep 17, 2017 at 11:02 AM, George Tzotzos <gtzotzos.me.com> wrote:
> I’ve run independent trajectories of subunits A and B of a homodimeric protein each of which is in complex with a ligand and a conserved water molecule (named HOH in the topology file) as shown below.
> subA-LIG-HOH
> subB-LIG-HOH
>
> Both systems are solvated. Due to oversight the order of LIG and HOH in the complex is reversed: subA-HOH-LIG-subB-HOH-LIG
>
> Trying to run MMGBSA following the multi-trajectory approach, I get the following error message
>
> PrmtopError: Couldn't predict mask from topology files!
> Your ligand residues must be sequential in your complex.
> There are likely problems with your topology files if this is not the case.
>
> My question is whether it is possible to modify the topology and trajectory of the complex (or subA/subB) to get around this problem.
>
> Thanks in advance for any suggestions
>
> George
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Sep 18 2017 - 06:00:16 PDT
