[gmx-users] Mismatching in Bergers DMPC bilayer lipid topology

[chris.neale at utoronto.ca]

Dear James:

Next time, please specify exactly what you did in enough detail for  
somebody else to reproduce it, much as in a manuscript. e.g. there is  
no "dmpc.gro" in that website. I can guess what you did, but that is  
not ideal.

I took a look at the files that I suppose you used and the atom names  
do appear to be mis-matched between the structure and the topology.  
That's is not necessarily a problem though. What happens if you set  
maxwarn to a large value during grompp and do a short mdrun? If that  
succeeds and looks normal, then I'd suggest to draw the structure of  
the lipid (about 50 atoms) and check out the topology by copying the  
names/charges/etc. onto your map.

I, for one, have used the dmpc.itp from that website and found that it  
is ok. I accessed the file years ago, so there is no guarantee it's  
the same file, but my topology also has names like NTM. I never did  
use that DMPC structure file though.

Chris.


-- original message --

Is here anobody who worked with the dmpc bilayers obtained from
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies


I've used this bilayers with the dmpc.itp and gromos96 ff with Berger lipids
and during loading my bilayer.gro in the grompt I've obtained warning about
mismatching in some atoms in .gro relatively .itp


Warning: atom name 1 in topol_dmpc.top and dmpc.gro does not match (CN1 -
CA)
Warning: atom name 2 in topol_dmpc.top and dmpc.gro does not match (CN2 -
CB)
Warning: atom name 3 in topol_dmpc.top and dmpc.gro does not match (CN3 -
CC)
Warning: atom name 4 in topol_dmpc.top and dmpc.gro does not match (NTM - N)
Warning: atom name 5 in topol_dmpc.top and dmpc.gro does not match (CA - CD)
Warning: atom name 6 in topol_dmpc.top and dmpc.gro does not match (CB - CE)
Warning: atom name 12 in topol_dmpc.top and dmpc.gro does not match (CC -
CF)
Warning: atom name 13 in topol_dmpc.top and dmpc.gro does not match (CD -
CG)
Warning: atom name 30 in topol_dmpc.top and dmpc.gro does not match (CE -
CH)
Warning: atom name 47 in topol_dmpc.top and dmpc.gro does not match (CN1 -
CA)
Warning: atom name 48 in topol_dmpc.top and dmpc.gro does not match (CN2 -
CB)
Warning: atom name 49 in topol_dmpc.top and dmpc.gro does not match (CN3 -
CC)
Warning: atom name 50 in topol_dmpc.top and dmpc.gro does not match (NTM -
N)
Warning: atom name 51 in topol_dmpc.top and dmpc.gro does not match (CA -
CD)
Warning: atom name 52 in topol_dmpc.top and dmpc.gro does not match (CB -
CE)
Warning: atom name 58 in topol_dmpc.top and dmpc.gro does not match (CC -
CF)
Warning: atom name 59 in topol_dmpc.top and dmpc.gro does not match (CD -
CG)
Warning: atom name 76 in topol_dmpc.top and dmpc.gro does not match (CE -
CH)
Warning: atom name 93 in topol_dmpc.top and dmpc.gro does not match (CN1 -
CA)
Warning: atom name 94 in topol_dmpc.top and dmpc.gro does not match (CN2 -
CB)
(more than 20 non-matching atom names)

Does this warning harmfull ? :)

JAmes
-