From: Mohammad Mehdi Pirnia (mpdezfouli_at_gmail.com)
Date: Sat Aug 21 2021 - 19:43:21 CDT
Hello all,
I'm simulating peptide interactions with a bacterial membrane. I used
https://urldefense.com/v3/__http://www.charmm-gui.org__;!!DZ3fjg!sUHTw_ttSkV751JXFMZIn6vCaaIjvm4ZuAOZekC-qEyR14duGO4yelVtnRtpgpvn0Q$ in order to get my membrane and it includes LPSA, PMCL,
PMPE, PMPG, PVPE, and PVPG.
1- Is it a way to create such membranes using VMD? I just saw POPC and POPE
in the membrane builder.
2- After download, I modified all residues' res-number to be consecutive,
they were repetitive. Now, I'm trying to create my membrane's PSF file.
Some parts of the output are shown below. I have shared the line of the
whole output (output.log), psf-creator (memb_psf.tcl), related stream
files, and the pdb file (semi_final_membrane.pdb).
Here is the link:
https://urldefense.com/v3/__https://files.fm/u/bcvap3g8g__;!!DZ3fjg!sUHTw_ttSkV751JXFMZIn6vCaaIjvm4ZuAOZekC-qEyR14duGO4yelVtnRuL4FhcWw$
my VMD version is 1.9.4a.51
Thank you all
Sincerely
Adam Pirnia
*output (broken into parts by "..."):*
psfgen) >>>>>>>>>>>>>>> parameter set discussion forum <<<<<<<<<<<<<<<<<<
psfgen)
psfgen) Created by CHARMM version 32 1
psfgen) reading topology file ../temporary2/toppar_all36_lipid_lps.str
psfgen) reading topology from stream file
psfgen) Topology for lipidA from LPS
psfgen)
psfgen) duplicate bond C71 C72 in residue BCLIPA
psfgen) ERROR! Failed to parse bond statement. Line 2010: BOND CB3 OB3
OB3 C71 C71 C72 CB1 OA6 CA6 OA6
psfgen) duplicate bond C71 C72 in residue BCLIPB
psfgen) ERROR! Failed to parse bond statement. Line 2760: BOND CB3 OB3
OB3 C71 C71 C72 CB1 OA6 CA6 OA6
..
..
psfgen) reading topology file ../temporary2/toppar_all36_carb_imlab.str
psfgen) reading topology from stream file
psfgen) glycan chemical modification patches
psfgen)
psfgen) Created by CHARMM version 41 1
psfgen) duplicate bond C5 N5 in residue ANEU
psfgen) ERROR! Failed to parse bond statement. Line 6293: BOND C5 N5
N5 HN51 N5 HN52
psfgen) duplicate bond CE3 O31 in residue AMU2AC
psfgen) ERROR! Failed to parse bond statement. Line 8981: BOND CE3 O31
CE3 O32
..
..
psfgen) reading topology file ../temporary2/toppar_all36_lipid_bacterial.str
psfgen) Toppar stream file for Branched and Cyclic Chained lipids.
Following reading of
psfgen) top_all36_lipid.rtf
psfgen) and
psfgen) par_all36_lipid.rtf
psfgen)
psfgen) ERROR! FAILED TO RECOGNIZE SET. Line 22: set nat ?NATC
psfgen) ERROR! FAILED TO RECOGNIZE SET. Line 23: set app
psfgen) ERROR! FAILED TO RECOGNIZE IF. Line 27: if "@NAT" ne "?NATC" if
@nat ne 0 set app append
psfgen) reading topology from stream file
psfgen) cholesterol residues
psfgen)
psfgen) Created by CHARMM version 36 1
psfgen) skipping parameters in stream file
psfgen) new parameters
psfgen)
psfgen) reading topology file
./temporary2/toppar_all36_lipid_cardiolipin.str
psfgen) reading topology from stream file
2.0
psfgen) building segment M
psfgen) reading residues from pdb file semi_final_membrane.pdb
psfgen) extracted 582 residues from pdb file
Info: generating structure...
psfgen) unknown atom type H
psfgen) add atom failed in residue ECLI:1
Segmentation fault (core dumped)
All these errors are odd to me, I didn't see anything wrong with my stream
files and atom type H is definitely defined!
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