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PS lipid headgroup carboxylate improper varies
#37997 07/21/20 08:59 PM
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Hello,

I am trying to understand why some PS lipids are missing an improper on the headgroup carboxylate. For example, in the tarball called toppar_c36_jul20.tgz downloaded from http://mackerell.umaryland.edu/charmm_ff.shtml , that improper is missing for SAPS and all other PS lipids in this stream file: toppar_all36_lipid_miscellaneous.str , which has statements like this:
IMPR C21 O21 C22 O22 C31 O31 C32 O32

However, PS lipids like POPS in the file called top_all36_lipid.rtf have impropers like this:
IMPR C21 O21 C22 O22 C31 O31 C32 O32 C13 C12 O13B O13A

My working assumption is that somebody simply forgot to add this PS-specific improper when adding PS lipids to toppar_all36_lipid_miscellaneous.str, but it would be great if anybody has some insight on who developed the PS lipid parameters in this toppar_all36_lipid_miscellaneous.str file, what the associated publication is, and/or any reasoning for this absent headgroup improper.

Thank you for your help,
Chris.

Last edited by Chris Neale; 07/21/20 09:19 PM.
Re: PS lipid headgroup carboxylate improper varies
Chris Neale #37999 07/23/20 04:37 PM
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Yes, it looks like that improper was omitted when the files were created. I've updated toppar_c36_jul20.tgz with the correction. Thanks, alex


School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201

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