Hello all,
After investigating this issue, here's the summary:
The CHARMM-GUI files have a specific atom type and residue naming that can be converted via the charmmlipid2amber.x script. Please note that we found a bug with converting ions in this script. I'm attaching an updated version (v 1.1.1) to this email available for those who need it now.
charmmlipid2amber.x converts the file into a format that can be loaded into LEaP that changes the atom names, residue names, the order of the residues within a phospholipid, and adds TER cards. For future reference, the format that can be loaded into LEaP for Lipid11 is as follows:
T1
H1
T2
TER
T1
H1
T2
TER
...
When LEaP saves the prmtop and inpcrd for a Lipid11 structure, the bonds are correct. (We also verified if you use ambpdb to create a pdb from your prmtop and inpcrd, it will create a pdb with the correct TER cards.)
Now we found that that there are two "bugs". First, in LEaP, when using the "SavePdb" command on a lipid structure, the format of the created pdb file (which cannot be used by Lipid11):
T1
TER
H1
TER
T2
TER
T1
TER
H1
TER
T2
...
The second issue in ptraj when using the "trajout" command to save a pdb file, the format of the created pdb file is (which cannot be used by Lipid11):
T1
H1
T2
T1
H1
T2
...
We're working on contacting the right people to resolve those issues now. Thank you for your interest in Lipid11.
Ben Madej
Walker Molecular Dynamics Lab
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Received on Fri May 11 2012 - 12:30:02 PDT
