Dear Community,
I apologize for a possible repost but the thread I found didn't
quite answer the question I have so I'm hoping for a bit more clarification
on this thread:
http://archive.ambermd.org/202011/0013.html
I understand restraintmask options but charmm gui puts restraints in a way
I can't find the explanation for. I have 4 specific lipid molecules (SAPI24
res # 299, 305, 359, 389) that I want to have the same restraints as the
protein during equilibration. I am trying to treat these lipids as a ligand
and would like to release the protein the these lipids at the same time. So
I have a few questions on the block of code below as an example.
the term "Protein" is this a term that is found in a .itp file or can this
be anything to name the group being restrained? if it is a name I can make
up for the group do I have to match the name in any other places or files?
Is there a page with this selection language? The pages I found were for
restraintmask selection using : - . * symbols not the words below.
Protein posres
10.0
RES 1 379 380 525 526 904 905 1050 1051 1429 1430 1575 1576 1954 1955 2100
END
Membrane posres
2.5
FIND
P * * POPC
P * * SAPI24
SEARCH
RES 1 71799
END
If I can give a group name can I just add this section to the bottom after
the membrane group?
Pip2 posres
10.0
FIND
P * * SAPI24 !!!! how do I specifiy the residue numbers with this
language? P 299 * SAPI24 ?
SEARCH
RES 1 71799 !!!! Is it safe to search for the residue number in
the parm7 or psf files? 299? so 299 389 to select all residues named SAPI24
between 299 and 389? I'm assuming this is a loaded residue number though
which I'm not sure how to get and would be different than the numbering
I've listed as it is probably unique numbering? can I use parmed to find
this unique numbering that amber would use?
END
Sorry for the mostly repeated thread but I've been at it for a few days and
the I only found the ntr = 1 description with restraintmask language in the
manual but not this charmm gui language.
Thank you again for any help,
Ryan
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Received on Wed Jan 03 2024 - 18:00:02 PST
