Dear Amber users,
I have an MG ion in my gag-receptor complex. However after running mmpbsa
as I wrote before I was obtaining an mismatch error. The reason for that
was that the mmpbsa.py automatically strips from the trajectory certain
ions as well as magnesium ...
In _MMPBSA_normal_traj_cpptraj.out I found ...
Reading '../top.top' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
INPUT: Reading input from 'STDIN'
[trajin ../prod5.mdcrd 1 1000 1]
Reading '../prod5.mdcrd' as Amber NetCDF
[noprogress]
Progress bar will not be used during Run.
[strip :WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL]
STRIP: Stripping atoms in mask
[:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL]
My question is how to "un-strip" the MG? Is there any script file in
mmpbsa tool that I could edit?
Thanks in advance for any help or suggestions.
best
Ula
> On Fri, Jun 15, 2018, Urszula Uciechowska wrote:
>>
>> I checked the sander complex file and mmpbsa complains about the atom
>> mismatch, I do not really understand why there is an atom mismatch?
>
> This means the number of atoms in the coordinate file does not match the
> number of atoms in the corresponding prmtop file. Did you look at the
> both the coordinate and prmtop files? Do they (perhaps) differ by one
> atom?
>
> Second thing to do: generate the complex prmtop and trajectory files "by
> hand", not using any script. Compare what you get with the files that
> are generated by the script. Can you spot any differences?
>
>> FATAL: NATOM mismatch in coord and topology files
>>
>
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--------------------------------------------
Urszula Uciechowska PhD
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Abrahama 58
80-307 Gdańsk
Poland
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
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Received on Tue Jun 19 2018 - 03:00:02 PDT
