Dear Amber users !
I am preparing a pdb structure for simulation with amber using pdb4amber.
After the processing I noticed that all information regarding chains
in the initial pbs was removed while the both segments are still
separated by TER. Here is the log from the pdb4amber
----------Chains
The following (original) chains have been found:
A
B
---------- Alternate Locations (Original Residues!))
The following residues had alternate locations:
SER_117
-----------Non-standard-resnames
---------- Missing heavy atom(s)
None
The alternate coordinates have been discarded.
Only the first occurrence for each atom was kept.
Is it possible to retain chain information in the prepared system and
store it somewhere in the parmtop file ? If yes, would it be possible
to use the atom masks for chains A and B as two selections for
subsequent mmgbsa calculations ?
Many thanks in advance
Enrico
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Received on Tue Jul 04 2023 - 01:00:02 PDT
