Dear All
I am trying to use new amber lipid14 ff on my protein-membrane complex
system but i get strange results after running heating and equilibration
(1.5ns) step. The head group of POPC lipid molecules fall apart from the
tails and keep floating in water box above and below the z axes of
bilayer. I have run initial minimization using Amber and then switching
to NAMD using amber forcefields (ff12SB and LIPID14).
Although i find some warning in tleap while loading lipid-protein
complex but i can successfully prepare coordinate and topology files.
These warnings are as below:
Enter zPdbReadScan from call depth 0.
Warning: name change in pdb file residue 492 ;
this residue is split into OL and PC.
Warning: name change in pdb file residue 492 ;
this residue is split into PC and PA.
Warning: name change in pdb file residue 493 ;
this residue is split into OL and PC.
Warning: name change in pdb file residue 493 ;
this residue is split into PC and PA.
Warning: name change in pdb file residue 494 ;
so on ..........
and for proteins:
(Residue 1: ASP, Nonterminal, was not found in name map.)
(Residue 2: SER, Nonterminal, was not found in name map.)
(Residue 3: LEU, Nonterminal, was not found in name map.)
(Residue 4: VAL, Nonterminal, was not found in name map.)
(Residue 5: VAL, Nonterminal, was not found in name map.)
(Residue 6: LEU, Nonterminal, was not found in name map.)
(Residue 7: VAL, Nonterminal, was not found in name map.)
similarly for ions
(Residue 881: Na+, Nonterminal, was not found in name map.)
(Residue 882: Cl-, Nonterminal, was not found in name map.)
(Residue 883: Cl-, Nonterminal, was not found in name map.)
(Residue 884: Cl-, Nonterminal, was not found in name map.)
(Residue 885: Na+, Nonterminal, was not found in name map.)
(Residue 886: Na+, Nonterminal, was not found in name map.)
(Residue 887: Na+, Nonterminal, was not found in name map.)
(Residue 888: Na+, Nonterminal, was not found in name map.)
(Residue 889: Na+, Nonterminal, was not found in name map.)
for solvent
(Residue 1461: WAT, Nonterminal, was not found in name map.)
(Residue 1462: WAT, Nonterminal, was not found in name map.)
(Residue 1463: WAT, Nonterminal, was not found in name map.)
(Residue 1464: WAT, Nonterminal, was not found in name map.)
(Residue 1465: WAT, Nonterminal, was not found in name map.)
(Residue 1466: WAT, Nonterminal, was not found in name map.)
(Residue 1467: WAT, Nonterminal, was not found in name map.)
(Residue 1468: WAT, Nonterminal, was not found in name map.)
(Residue 1469: WAT, Nonterminal, was not found in name map.)
(Residue 1470: WAT, Nonterminal, was not found in name map.)
and for lipids :
(Residue 79964: PC, Terminal/last, was not found in name map.)
(Residue 79965: PA, Terminal/last, was not found in name map.)
(Residue 79966: OL, Terminal/last, was not found in name map.)
(Residue 79967: PC, Terminal/last, was not found in name map.)
(Residue 79968: PA, Terminal/last, was not found in name map.)
(Residue 79969: OL, Terminal/last, was not found in name map.)
(Residue 79970: PC, Terminal/last, was not found in name map.)
(Residue 79971: PA, Terminal/last, was not found in name map.)
(Residue 79972: OL, Terminal/last, was not found in name map.)
(Residue 79973: PC, Terminal/last, was not found in name map.)
(Residue 79974: PA, Terminal/last, was not found in name map.)
(Residue 79975: OL, Terminal/last, was not found in name map.)
(Residue 79976: PC, Terminal/last, was not found in name map.)
(Residue 79977: PA, Terminal/last, was not found in name map.)
Is there something wrong with my initial coordinate and topology files?
as it seems there is no connectivity between head and tail groups, and
also there is TER flag introduced by tleap between each tail, head and
tail molecules.
Looking for your kind input in this regard
Mustafa
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Received on Thu Mar 20 2014 - 09:00:03 PDT
