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additive C36 all-atom lipid parameters
#24475 06/02/10 07:16 PM
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alex Offline OP
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Hello,

The new additive C36 all-atom lipid parameters may now be obtained from our web page (see below). The parameters yield the correct surface area per head group for a number of lipid bilayers and are compatible with the the additive CHARMM all-atom parameters for proteins, nucleic acids, carbohydrates and general organic molecules (CGenFF). It should be emphasized that this compatibility is based on CHARMM consistent force field parameter optimization. Use of parameters from other force fields in combination with the CHARMM parameters, including partial atomic charges, may lead to lower quality results is simulation studies of heterogenous systems. Below is the web page force fields as well as the reference for the C36 lipid paper.

alex

All force fields

http://mackerell.umaryland.edu/CHARMM_ff_params.html

C36 lipid force field

http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_lipid_all36.tgz

Reference

Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types" J. Phys. Chem. B, Articles ASAP (As Soon As Publishable) Publication Date (Web): May 24, 2010 (Article) DOI: 10.1021/jp101759q


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Re: additive C36 all-atom lipid parameters
alex #24663 06/24/10 01:44 AM
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The final reference is: J. Phys. Chem. B 2010, 114, 7830-7843

Bilayer coordinate sets, spaced at 1 ns intervals, from the last 20 ns of the NPT simulations in the paper for DLPC, DMPC, DPPC, POPC and DOPC are available here. There are two tar archives (.tgz) for each lipid type, one with CHARMM format coordinate files, the other with PDB format coordinate files. Molecule counts and unit cell sizes are in the title records of each coordinate file.


Rick Venable
computational chemist

Re: additive C36 all-atom lipid parameters
rmv #24978 07/29/10 05:44 PM
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Bug note:

Due to a late change, there's an atom chemical type naming error for the DOPC and POPC residues in the file lipid_convert/toppar_all36_lipid_oldxopc.str

For each residue, the two lines

ATOM O1 OSP -0.57 ! / \
ATOM O2 OSP -0.57 ! (-) O4 O2

should be changed to

ATOM O1 OSLP -0.57 ! / \
ATOM O2 OSLP -0.57 ! (-) O4 O2


Usage note:

For applications other than CHARMM, users with pre-existing coordinate sets may wish to edit (a copy of) the RTF file, replacing the new DOPC or POPC definition with the one(s) in the stream file indicated above. Also, for the rename, the "convert" script shows the equivalent names, and could probably be readily accomplished via a variety of text processing scripted languages (which would make a good donation to the Script Archive).


Rick Venable
computational chemist

Re: additive C36 all-atom lipid parameters
rmv #25103 08/11/10 07:13 PM
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I've added a general 'sed' script in the Script Archive which does the alpha chain atom renames for DOPC and POPC; it should work on any coordinate file format with one atom per text line, and which includes the residue name on each line (e.g. PDB or COOR CARD).


Rick Venable
computational chemist

Re: additive C36 all-atom lipid parameters
rmv #34296 08/15/14 11:19 PM
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Hi,

I work extensively with VMD, the latest version of which uses C27 force field for proteins lipids and nucleic acids, but the c36 for lipids is also present (both topology and parameters).

The publication J. Phys. Chem. B, 2010, 114 (23), pp 7830–7843, indicates if I didn't over look anything that only lipids are effected between C27 and C36.

This shows that working on proteins (only) today with C27 should be ok.

However before starting my new work I randomly manually checked (just to be on the safe side) if there were any differences between C27 and C36 for the protein residues.

The grouping of the side chain atoms between TRP across the two force fields is not consistent, where C27 groups atoms on the side chains across all residues, C36 doesn't for the residue "TRP".

Can someone comment on this?

Best,

p.s. i did search the forum before posting if someone had written about this before, however searching keywords like charmm36, c36 and force field didn't generate anything relevant. If I missed something out and this is a repost, I apologize.


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/Spooky
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Re: additive C36 all-atom lipid parameters
alex #34297 08/16/14 12:22 AM
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Sigh.

There is no C27 protein force field, there is only C22 and C22/CMAP; the file naming of legacy combined files such as "all27_prot_lipid" has created some confusion, and consequently the NAMD people may be spreading incorrect version information. The correct version numbers can be identified in complete distributions of the CHARMM topology and parameter files by looking at the name of protein-only files, which has been "all22_prot" or "all22_prot_cmap" until recently.

All topology and parameter files are now essentially C36, which implies at least a conversion to CHARMM's FLEX file format, but for proteins includes changes for both backbone and sidechain dihedrals.

See this sticky post; "sticky" posts are always displayed at the top of the list of posts for each forum.


Rick Venable
computational chemist

Re: additive C36 all-atom lipid parameters
rmv #34298 08/16/14 01:11 AM
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Yes. I am aware of the naming convention, apologies on not being clear in the previous post.

Let me put the question in another way.

In the latest update to the forcefield, correcting lipid parameters, topology file for proteins sees the side chain atoms of all the residues separated into groups for the purpose of charge distribution except Tryptophan.

i.e. If you look at any other residue for example tyrosine

RESI TYR 0.00
GROUP
ATOM N NH1 -0.47 ! | HD1 HE1
ATOM HN H 0.31 ! HN-N | |
ATOM CA CT1 0.07 ! | HB1 CD1--CE1
ATOM HA HB1 0.09 ! | | // \\
GROUP ! HA-CA--CB--CG CZ--OH
ATOM CB CT2 -0.18 ! | | \ __ / \
ATOM HB1 HA2 0.09 ! | HB2 CD2--CE2 HH
ATOM HB2 HA2 0.09 ! O=C | |
GROUP ! | HD2 HE2
ATOM CG CA 0.00
GROUP
ATOM CD1 CA -0.115
ATOM HD1 HP 0.115
GROUP
ATOM CE1 CA -0.115
ATOM HE1 HP 0.115
GROUP
ATOM CZ CA 0.11
ATOM OH OH1 -0.54
ATOM HH H 0.43
GROUP
ATOM CD2 CA -0.115
ATOM HD2 HP 0.115
GROUP
ATOM CE2 CA -0.115
ATOM HE2 HP 0.115
GROUP
ATOM C C 0.51
ATOM O O -0.51

-----------------------------------------------------
Now in the same file, Tryptophan:

RESI TRP 0.00
GROUP
ATOM N NH1 -0.47 ! | HE3
ATOM HN H 0.31 ! HN-N |
ATOM CA CT1 0.07 ! | HB1 CE3
ATOM HA HB1 0.09 ! | | / \\
GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3
ATOM CB CT2 -0.18 ! | | || || |
ATOM HB1 HA2 0.09 ! | HB2 CD1 CE2 CH2-HH2
ATOM HB2 HA2 0.09 ! O=C / \ / \ //
GROUP ! | HD1 NE1 CZ2
ATOM CG CY -0.03 ! | |
ATOM CD1 CA -0.15 ! HE1 HZ2
ATOM HD1 HP 0.22
ATOM NE1 NY -0.51
ATOM HE1 H 0.37
ATOM CE2 CPT 0.24
ATOM CD2 CPT 0.11
ATOM CE3 CAI -0.25
ATOM HE3 HP 0.17
ATOM CZ3 CA -0.20
ATOM HZ3 HP 0.14
ATOM CZ2 CAI -0.27
ATOM HZ2 HP 0.16
ATOM CH2 CA -0.14
ATOM HH2 HP 0.14
GROUP
ATOM C C 0.51
ATOM O O -0.51

------------------------------------------------

I would like to understand why there exists a difference only for this residue? (This is more of a chemistry based question i.e. what makes Tryptophans side chain different chemically ).

Best,

Last edited by spooky; 08/16/14 01:20 AM.

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/Spooky
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Re: additive C36 all-atom lipid parameters
alex #34300 08/16/14 02:07 AM
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The GROUPs should have an integer charge, e.g. 0, -1, or +1; the change for TRP suggests that the side chain charges may be different for C36. A quick comparison of the TRP residues from C22 and C36 shows that the atom charges have changed.

BTW, the C36 protein citation is Journal of Chemical Theory and Computation 2012, 8(9), 3257-3273.


Rick Venable
computational chemist

Re: additive C36 all-atom lipid parameters
alex #34337 08/25/14 04:28 PM
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Just to make things absolutely clear: the CHARMM36 force field features substantial updates to the protein, nucleic acid and lipid paramter sets. <shameless plug>We just wrote a review on the subject.</shameless plug>

Last edited by Kenno; 08/25/14 04:29 PM. Reason: no HTML preview.

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