Thank you. Are these ONLY the atoms intended for remapping or atoms of residues 1-end?
George
> On 18 Sep 2017, at 16:01, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> No, it's atoms. I haven't implemented a by residue mode for remap yet.
>
> -Dan
>
> On Mon, Sep 18, 2017 at 8:53 AM, George Tzotzos <gtzotzos.me.com> wrote:
>> 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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Sep 18 2017 - 06:30:04 PDT
