From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Oct 31 2014 - 15:37:42 CDT

Dear Chaya,

You can not have a ACE on Aspartate. Aspartate has a charge of -1. ACE
would make it have no charge. Your first residue being charged would not
allow you to use ACE. You either need to do use autopsf gen in which case
it would assign it a patch of ASPP or if you choose to do it manually which
is not a good idea at a beginner level - use PRES ASPP.

Hope this helps.

Good luck.

Best,
/A

On Sat, Nov 1, 2014 at 8:08 AM, Chaya Stern <chaya.stern_at_choderalab.org>
wrote:

> Hello,
>
> 'm trying to add the ACE patch to the N-terminal but it seems like psfgen
> is not finding the HN atom.
>
> Here are the residue in the pdb:
> ATOM 1 N ASP P 23 18.447 -22.433 28.702 1.00
> 0.00 PROT N
> 7 ATOM 2 HN ASP P 23 18.888 -23.323 28.586 1.00
> 0.00 PROT H
> 8 ATOM 3 CA ASP P 23 19.440 -21.467 29.166 1.00
> 0.00 PROT C
> 9 ATOM 4 HA ASP P 23 19.773 -21.804 30.141 1.00
> 0.00 PROT H
> 10 ATOM 5 CB ASP P 23 20.644 -21.408 28.204 1.00
> 0.00 PROT C
> 11 ATOM 6 HB1 ASP P 23 21.374 -20.663 28.578 1.00
> 0.00 PROT H
> 12 ATOM 7 HB2 ASP P 23 21.149 -22.393 28.149 1.00
> 0.00 PROT H
> 13 ATOM 8 CG ASP P 23 20.299 -20.994 26.784 1.00
> 0.00 PROT C
> 14 ATOM 9 OD1 ASP P 23 20.550 -19.822 26.432 1.00
> 0.00 PROT O
> 15 ATOM 10 OD2 ASP P 23 19.753 -21.834 26.037 1.00
> 0.00 PROT O
> 16 ATOM 11 C ASP P 23 18.828 -20.078 29.364 1.00
> 0.00 PROT C
> 17 ATOM 12 O ASP P 23 18.139 -19.579 28.474 1.00
> 0.00 PROT O
>
> When I try to generate the patch for this residue, these are the errors I
> get:
>
> psfgen) building segment PROT
> 94 psfgen) reading residues from pdb file ../pdb_files/frag0_protien.pdb
> 95 psfgen) extracted 310 residues from pdb file
> 96 psfgen) Info: generating structure...psfgen) Info: skipping improper
> N-C-CA-HN at beginning of segment.
> 97 psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of
> segment.
> 98 psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
> 99 psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
> 100 psfgen) ERROR: Missing atoms for bond C(0) N(1) in residue ARG:344
> 101 psfgen) ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
> 102 in residue ARG:344
> 103 psfgen) ERROR: Missing atoms for cross-term C(-1) N(0) CA(0) C(0)
> N(0) CA(0) C(0) N(1)
> 104 in residue ARG:344
> 105 psfgen) Warning: missing atoms for conformation ARG CA-C-N-CA;
> skipping.
> 106 psfgen) Warning: missing atoms for conformation ARG N-CA-C-O; skipping.
> 107 psfgen) Warning: missing atoms for conformation ARG N-CA-C-N; skipping.
> 108 segment complete.
> 109 psfgen) reading coordinates from pdb file
> ../pdb_files/frag0_protien.pdb for segment PROT
> 110 psfgen) Warning: failed to set coordinate for atom HN ASP:23 PROT
> 111 psfgen) Warning: failed to set coordinate for atom HE2
> GLU:122 PROT
> 112 psfgen) Warning: failed to set coordinate for atom OT1
> ARG:344 PROT
> 113 psfgen) Warning: failed to set coordinate for atom OT2
> ARG:344 PROT
> 114 psfgen) applying patch DISU to 2 residues
> 115 psfgen) applying patch DISU to 2 residues
> 116 psfgen) applying patch GLUP to 1 residues
> 117 psfgen) applying patch PLCY to 2 residues
> 118 psfgen) applying patch ACE to 1 residues
> 119 psfgen) no atom HN in residue ASP:23 of segment PROT
> 120 psfgen) Warning: add improper failed in patch ACE
> 121 psfgen) no atom HN in residue ASP:23 of segment PROT
> 122 psfgen) Warning: add conformation failed in patch ACE
> 123 psfgen) applying patch CT3 to 1 residues
>
>
> This is what the resulting pdb looks like:
> ATOM 1 CAY ASP P 23 17.036 -23.161 29.064 0.00
> 0.00 PROT
> 3 ATOM 2 HY1 ASP P 23 17.325 -23.525 28.178 0.00
> 0.00 PROT
> 4 ATOM 3 HY2 ASP P 23 16.153 -22.702 28.972 0.00
> 0.00 PROT
> 5 ATOM 4 HY3 ASP P 23 16.968 -23.903 29.730 0.00
> 0.00 PROT
> *6 ATOM 5 CY ASP P 23 17.716 -22.500 29.381 0.00
> 0.00 PROT*
> 7 ATOM 6 OY ASP P 23 17.428 -22.137 30.267 0.00
> 0.00 PROT
> 8 ATOM 7 N ASP P 23 18.447 -22.433 28.702 1.00
> 0.00 PROT N
> 9 ATOM 8 HT1 ASP P 23 18.888 -23.323 28.586 0.00
> 0.00 PROT
> 10 ATOM 9 HT2 ASP P 23 18.073 -22.122 27.828 0.00
> 0.00 PROT
> *11 ATOM 10 HT3 ASP P 23 17.716 -22.500 29.381 0.00
> 0.00 PROT*
> 12 ATOM 11 CA ASP P 23 19.440 -21.467 29.166 1.00
> 0.00 PROT C
> 13 ATOM 12 HA ASP P 23 19.773 -21.804 30.141 1.00
> 0.00 PROT H
> 14 ATOM 13 CB ASP P 23 20.644 -21.408 28.204 1.00
> 0.00 PROT C
>
> It places a CY and HT3 in the same spot. There's an HN in the topology
> file for residue ASP so I don't know why psfgen is not finding it. It seems
> like both the default and ACE termini are added here.
>
> Thank you!
>
>

-- 
Best,
/A