No, it has to be all atoms currently - unfortunately the command isn't
very user-friendly at this point. Your questions have given me some
ideas how to improve the command. I'll try and implement some of the
ideas this week.
Thanks,
-Dan
On Mon, Sep 18, 2017 at 9:04 AM, George Tzotzos <gtzotzos.me.com> wrote:
> 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
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> _______________________________________________
>>> 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
>
>
> _______________________________________________
> 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
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Received on Mon Sep 18 2017 - 12:30:01 PDT
