From: Chaya Stern (chaya.stern_at_choderalab.org)
Date: Mon Nov 03 2014 - 11:17:08 CST

It's true that when I put it inside the segment it works, but I to apply a
different patch to attach PALM to a CYS and if I don't apply the patch
first, the last command tries to apply the CT3 patch to PALM which occurs
right after the last residue in the pdb. What I find really weird is that
while I'm having trouble attaching the ACE patch after the segment is
built, The same problem doesn't come up for the C terminal. Why is that?

Because I don't have a problem applying the CT3 patch, I only applied the
ACE patch inside the segment command, then attached the PALM to the CYS and
then applied the CT3 patch. It seems to work but I do have some warnings

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) setting patch for first residue to ACE
 97 psfgen) Info: generating structure...psfgen) Info: skipping improper
N-C-CA-HN at beginning of segment.
 98 psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of
segment.
 99 psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
100 psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
101 psfgen) ERROR: Missing atoms for bond C(0) N(1) in residue ARG:344
102 psfgen) ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
103 in residue ARG:344
104 psfgen) ERROR: Missing atoms for cross-term C(-1) N(0) CA(0) C(0) N(0)
CA(0) C(0) N(1)
105 in residue ARG:344
106 psfgen) Warning: missing atoms for conformation ARG CA-C-N-CA; skipping.
107 psfgen) Warning: missing atoms for conformation ARG N-CA-C-O; skipping.
108 psfgen) Warning: missing atoms for conformation ARG N-CA-C-N; skipping.
109 segment complete.
110 psfgen) reading coordinates from pdb file
./pdb_files/frag0_protien.pdb for segment 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 CT3 to 1 residues
119 psfgen) building segment CHL1
120 psfgen) reading residues from pdb file ../pdb_files/frag1_CHL.pdb
121 psfgen) extracted 16 residues from pdb file
122 psfgen) Info: generating structure...segment complete.
123 psfgen) reading coordinates from pdb file ../pdb_files/frag1_CHL.pdb
124 psfgen) building segment MEMB
125 psfgen) reading residues from pdb file ../pdb_files/frag2_BDDM.pdb
126 psfgen) extracted 154 residues from pdb file
127 psfgen) Info: generating structure...segment complete.
128 psfgen) reading coordinates from pdb file ../pdb_files/frag2_BDDM.pdb
129 psfgen) regenerating all angles
130 psfgen) regenerating all dihedrals
131 psfgen) Info: guessing coordinates for 14 atoms (6 non-hydrogen)
132 psfgen) Warning: poorly guessed coordinates for 14 atoms (6
non-hydrogen):
133 psfgen) Warning: poorly guessed coordinate for atom CAY ASP:23 PROT
134 psfgen) Warning: poorly guessed coordinate for atom HY1 ASP:23 PROT
135 psfgen) Warning: poorly guessed coordinate for atom HY2 ASP:23 PROT
136 psfgen) Warning: poorly guessed coordinate for atom HY3 ASP:23 PROT
137 psfgen) Warning: poorly guessed coordinate for atom CY ASP:23 PROT
138 psfgen) Warning: poorly guessed coordinate for atom OY ASP:23 PROT
139 psfgen) Warning: poorly guessed coordinate for atom HE2
GLU:122 PROT
140 psfgen) Warning: poorly guessed coordinate for atom O
ARG:344 PROT
141 psfgen) Warning: poorly guessed coordinate for atom NT
ARG:344 PROT
142 psfgen) Warning: poorly guessed coordinate for atom HNT
ARG:344 PROT
143 psfgen) Warning: poorly guessed coordinate for atom CAT
ARG:344 PROT
144 psfgen) Warning: poorly guessed coordinate for atom HT1
ARG:344 PROT
145 psfgen) Warning: poorly guessed coordinate for atom HT2
ARG:344 PROT
146 psfgen) Warning: poorly guessed coordinate for atom HT3
ARG:344 PROT

When I check the poorly guessed coordinates, the angles look a little weird
but I believe these can be corrected with a minimization. However, how do I
ensure that these warnings shouldn't come up?

On Fri, Oct 31, 2014 at 5:41 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> How are you trying to apply the ACE patch? It needs to happen inside the
> segment command, not after it like you would for a disulfide, since the
> segment patches need to be altered.
>
> segment PROT {
> pdb ../pdb_files/frag0_protien.pdb
> first ACE
> last CTER
> }
>
> By default, the first patch is assumed to be NTER, so if you wait until
> after the segment is generated, the NTER patch has already been applied,
> and as you found out, you can't apply both.
>
> -Josh Vermaas
>
>
> On 10/31/2014 02:08 PM, Chaya Stern 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!
>
>
>