GROMACS version: 2022.1
GROMACS modification: No
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Dear experts. If you have any experience in using membrane other than PC membrane, may I ask your advice?
I’m trying to use PG membrane. Although that membrane doesn’t be distributed from D. Peter Tielemanin’s webpage, I was lucky to find other generous distributors such as SLipid or Softsimu.
http://www.fos.su.se/~sasha/SLipids/Downloads.html
https://www.softsimu.net/downloads.shtml
There is no problem simulating those membranes alone.
But a problem arise when I tried to make peptide-membrane united-atom force field.
Either when I use SLipid or simu, I confront different problems.
In the case of Slipid, I used amber99sb-ildn.ff, as recommended by distributors.
However, the parameter or atom names of member99sb-idn.ff and Slipid overlap too much, but the contents are different.
For example:
amber99sb-ildn.ff.atp : H 1.00800 ; H bonded to nitrogen atoms
SLipidff.atp : H 1.00800 ; polar H
amber99sb-ildn.ff.atp : HC 1.00800 ; H aliph. bond. to C without electrwd.group
SLipidff.atp : HC 1.00800 ; N-ter H
amber99sb-ildn.ff.atp : HA 1.00800 ; H arom. bond. to C without elctrwd. groups
SLipidff.atp : HA 1.00800 ; nonpolar H
amber99sb-ildn.ff.atp : CA 12.01000 ;sp2 C pure aromatic (benzene)
SLipidff.atp : CA 12.01100 ;aromatic C
In the case of simu, I used lipid.itp from Peter Tieleman’s website, as recommended by distributors.
However, Simu’s distributed itp and pdb files contains HO, which does not exist in gromos53a6_lipid.ff parameters.
So Error message shown
ERROR 1 [file popg.itp, line 23]:
Atomtype HO not found
So I replaced ‘HO’ in popg.itp and popg.pdb to ‘H’ but this trial resulted completely broken image
For expert, have you been crossed with problems as I did? If then, may I ask how you solved such problem?
Thanks for your time and attention.
amber99sb-ildn.ff -atomtypes.top (3.7 KB)
Slipids_2020.ff -atomtypes.top (10.8 KB)
gromos53a6_lipid.ff -ffnonbonded.itp.top (150.9 KB)
softsimu popg itp.top (29.4 KB)