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21

can you explain “introduce by analogy”?
am I correct in understanding I can build the RTP from cys glu and gly along with adding for the S-S atoms which I can find in the atomtypes file?
then if I used the atom types of traditional AA i should only have at most a few dihedrals to address which I can write by looking through the ffbonded file and finding a similar set of bonds applying my specific atom types to add to my missing dihedrals.itp

22

Look at existing residues and assign the same atom types and charges for chemically equivalent (or sufficiently similar moieties).

Yes.

Correct.

23

I rewrote my rtp exclusively using atom types from glu asp gly cys as to avoid writing new bonded parameters

;Gutathionylated cysteine +1
  [ atoms ]
        N      NH1 -0.6300   1  
      HN0        H  0.3600   2
       CA      CT1  0.3310   3
       HA      HB1  0.0000   4
       CB      CT2  0.2300   5
      HB1      HA2  0.0000   6
      HB2      HA2  0.0000   7
       SG       SM -0.2300   8
       SD       SM -0.2300   9
       CY      CT2  0.2300  10
      HY1      HA2  0.0000  11
      HY2      HA2  0.0000  12
       CD      CT1  0.5640  13  ; aliphatic C with 1 H, CH
       HD      HB1  0.0000  14; alkane, CH,
       NB      NH3 -0.7990  15
      HN1        H  0.4500  16
      HN2        H  0.4500  16
       CE        C  0.9050  17    ; carbonyl C: [negative] carboxylates
       OE        O -0.5700  18   ; carbonyl O: negative groups: carboxylates, carbonate
       CF      CT2  0.0610  19  ;ch2
      HF1      HA2  0.0000  20  ;alphatic proton, CH2
      HF2      HA2  0.0000  22   ;alphatic proton, CH2
       CH      CT2  0.0000  23   ;ch2
      HH1      HA2  0.0000  24  ;alphatic proton, CH2
      HH2      HA2  0.0000  25   ;alphatic proton, CH2
       CM      CT1  0.3970  26  ; aliphatic sp3 C for CH
       HG      HA1  0.0000  27   ; alphatic proton, CH
       NY      NH3 -0.8530  28; ammoniumide nitrogen
      HN3       HC  0.4500  29   ; polar H
      HN4       HC  0.4500  30   ; polar H
      HN5       HC  0.4500  31  
       CJ        C  0.9060  32    ; carbonyl C: [negative] carboxylates
       OF       OC -0.9000  33   ; carbonyl O: negative groups: carboxylates, carbonate
       OG       OC -0.9000  34   ; carbonyl O: negative groups: carboxylates, carbonate
       CL        C  0.9050  35    ; carbonyl C: [negative] carboxylates
       OI        O -0.5700  36   ; carbonyl O: negative groups: carboxylates, carbonate
       NZ      NH3 -0.7990  37
      HZ1        H  0.4500  38
      HZ2        H  0.4500  39
       CQ      CT2  0.3970  40  ;ch2
      HQ1      HA2  0.0000  41  ;alphatic proton, CH2
      HQ2      HA2  0.0000  42   ;alphatic proton, CH2
       CZ        C  0.9060  43    ; carbonyl C: [negative] carboxylates
       OM       OC -0.9000  44   ; carbonyl O: negative groups: carboxylates, carbonate
       ON       OC -0.9000  45   ; carbonyl O: negative groups: carboxylates, carbonate
        C        C  0.5090  46
        O        O -0.5700  47
  [ bonds ]
       CB    CA
       SG    CB
        N   HN0
        N    CA
        C    CA
        C    +N
       CA    HA
       CB   HB1
       CB   HB2
       CB    SG
       SG    SD
       SD    CY
       CY   HY1
       CY   HY2
       CY    CD
       CD    HD
       CD    NB
       CD    CL
       NB   HN1
       NB   HN2
       NB    CE
       CE    OE
       CE    CF
       CF   HF1
       CF   HF2
       CF    CH
       CH   HH1
       CH   HH2
       CH    CM
       CM    HG
       CM    NY
       CM    CJ
       NY   HN3
       NY   HN4
       NY   HN5
       CJ    OF
       CJ    OG
       CL    OI
       CL    NZ
       NZ   HZ1
       NZ   HZ2
       NZ    CQ
       CQ   HQ1
       CQ   HQ2
       CQ    CZ
       CZ    OM
       CZ    ON
        O     C
  [ impropers ]
        N    -C    CA    HN
        C    CA    +N     O
       CL    NZ    CD    OI ;  carbonyl c 
       CL    CD    NZ    OI  ;carbonyl c
       CZ    CF    ON    OM  ; carboxylic 
       CJ    CM    OG    OF ; carboxylic 
       CE    CF    NB    OE;  carbonyl c
       CE    NB    CF    OE;  carbonyl c
  [ cmap ]
       -C     N    CA     C    +N

I am able to assemble my .gro but when I try to run gromp to make my ions.tpr there are 65 errors about missing bonded and unbonded and dihedrals.

ERROR 1 [file topol.top, line 10020]:
  No default Bond types

ERROR 26 [file topol.top, line 36965]:
  No default U-B types

ERROR 63 [file topol.top, line 51688]:
  No default Proper Dih. types

Fatal error:
There were 65 errors in input file(s)

I believe this is refering to the bonds pairs angles and dihedrals that are produced by swissparam or cgenff. How would you advise I resolve these errors.
is there a simpler way than addressing all 65 one by one finding the match in the topol then looking it up in the .gro then matching it to my itp and entering it in my ffbonded.itp one by one?

24

If you’re using all standard residue definitions and atom types from CHARMM, I have no idea how CGenFF or SwissParam would even factor in here. Aren’t you using pdb2gmx to produce the entire topology once you have written the .rtp entry?

25

Yes, I used pdb2gmx. I used swissparam to determine charges as to avoid a qtot that is a float when assembling my rtp.

26

You should be getting the charges from the existing residue definitions, but even so, the charge assignment has nothing to do with missing bonded parameters, which I find odd. Please report back about what a few of the missing bonds are.