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
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> 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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--
-------------------------
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 - 06:30:03 PDT
