Thank you Dan, most helpful.
One last question. Is remap.dat a two column file of residues, that is res.ID 1 to end?
George
> On 18 Sep 2017, at 15:38, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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 - 06:00:17 PDT
