Hi:
I must have a some conceptually wrong steps in a LEaP (ambertools12)
procedure for getting prmtop/inpcrd for a protein inglobating
covalently a lipidic residue.
1) I removed aa residues 41-44, leaving a hole between T40 and P45,
placed in between the lipid, got a mol2 file with RESP charges. This
new single residue RES, alongside frcmod for the mol2, got with
parmchk) gave correct prmtop/inpcrd.
2) I loaded to LEaP that mol2 file, the related frcmods, and the pdb
file (with vacant residues) , LEaP renumbered from zero and created a
bond at the vacant position between 39 and 40
(Residue 38: TYR, Nonterminal, was not found in name map.)
(Residue 39: THR, Nonterminal, was not found in name map.)
(Residue 40: PRO, Nonterminal, was not found in name map.)
(Residue 41: LEU, Nonterminal, was not found in name map.)
(Residue 42: ALA, Nonterminal, was not found in name map.)
Joining TYR - THR
Joining THR - PRO
Joining PRO - LEU
Joining LEU - ALA
and did not allow me creating bonds between the protein and RES (only
the first few atoms of RES are seen by comman "desc" and with other
than desired bonding):.
3) I Placed a TER line between resid 40 and 45 before repeating the
procedure at 2). Now LEaP created a new atom OXT for THR39 and, again,
RES was not seen as I desired by command "desc", so that no "bond"
could be carried out.
As such, RES, a single residue for 4 aa and a lipid, can not be
inserted between 41 and 44.
I would be very grateful for suggesting what to change in the procedure.
Incidentally, I have reparameterized a whole bunch of aa containing
the lipid, instead of the lipid alone, to try to take into account the
conformational changes that ensue the reaction of the protein.
Thanks
francesco pietra
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Received on Fri Jul 20 2012 - 07:00:02 PDT
