[gmx-users] Re: [gmx-developers] building block in rtp file

[Alexandre Suman de Araujo]

Lakshmi Padmavathi wrote:

>Dear gromacs users,
>
>i would like to make one building block for a abnormal residue (not usual 
>aminoacid but has aminoacid properties).
>
>so,i creatred one building block. i inserted in ffgmx.rtp, ffgmx.hdb and in
>aminoacids.dat. i am using ffgmx forcefield ( option "0" of the forcefield)
>
>but it couldnot recognise the file in rtp database when i run pdb2gmx.
>
>for testing, i replaced the ALA (alanine) with YYY in rtpfile,hdb and 
>aminoacid.dat file. i have given the alannin pdb coordinates. but it is still 
>not recognising if i change just the name.
>
>I am changing the residue name in pdb file also.
>
>i request you all to give suggestion for this.
>
>i will be very thankful to you. 
>
>i will pastet he error of pdb2gmx here.
>
> 
>------------------------------------------------------------------------------------------------------
>Opening library file /usr/local/share/gromacs/top/xlateat.dat
>13 out of 13 lines of xlateat.dat converted succesfully
>Opening library file /usr/local/share/gromacs/top/aminoacids.dat
>Analyzing pdb file
>There are 1 chains and 0 blocks of water and 1 residues with 5 atoms
>
>  chain  #res #atoms
>  1 ' '     1      5
>
>All occupancies are one
>Opening library file /usr/local/share/gromacs/top/FF.dat
>
>Select the Force Field:
> 0: Gromacs Forcefield (see manual)
> 1: Gromacs Forcefield with all hydrogens (proteins only)
> 2: GROMOS96 43a1 Forcefield (official distribution)
> 3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
> 4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>0
>Using ffgmx force field
>Opening library file /usr/local/share/gromacs/top/ffgmx.atp
>Atomtype 52
>Reading residue database... (ffgmx)
>Opening library file /usr/local/share/gromacs/top/ffgmx.rtp
>Using default value - not generating all possible dihedrals
>Using default value - excluding 3 bonded neighbors
>Residue 97
>Sorting it all out...
>Opening library file /usr/local/share/gromacs/top/ffgmx.hdb
>Opening library file /usr/local/share/gromacs/top/ffgmx-n.tdb
>Opening library file /usr/local/share/gromacs/top/ffgmx-c.tdb
>
>Back Off! I just backed up test.top to ./#test.top.5#
>Processing chain 1 (5 atoms, 1 residues)
>Opening library file /usr/local/share/gromacs/top/specbond.dat
>5 out of 5 lines of specbond.dat converted succesfully
>There are 1 donors and 1 acceptors
>There are 1 hydrogen bonds
>Fatal error: Residue 'YYY' not found in residue topology database
>
>
>i paste my building block here.
>
>[ XXX ]
> [ atoms ]
>     N     N  -0.280     0
>     H     H   0.280     0
>    CA   CH1   0.000     1
>    CB   CH2   0.000     2
>    S1     S   0.000     3
>     S     S   0.000     4
>    C9   CH2   0.000=09 5
>    C8   CH3   0.000     6
>    C7   CH3   0.000     7
>    C6   CH3   0.000     8
>    C5   CH3   0.000     9
>    C4    CB   0.110    10
>    N1  NR5*   0.080    10
>    OH     O  -0.300    10
>    C1    CB   0.110    10
>    C2    CB   0.000    11
>    C3   CR5   0.000    12
>     C     C   0.380     4
>     O     O  -0.380     4
> [ bonds ]
>     N     H
>     N    CA
>    CA     C
>     C     O
>    -C     N
>    CA    CB
>    CB    S1
>    S1     S
>     S    C9
>    C9    C2
>    C2    C3
>    C3    C4
>    C6    C4
>    C5    C4
>    C4    N1
>    OH    N1
>    C2    C1
>    N1    C1
>    C8    C1
>    C1    C7
> [ impropers ]
>     N    -C    CA     H
>    -C   -CA     N    -O
>    CA     N     C    CB
>    N1    C1    OH    C4
>    C2    C1    C3    C9
>    C1    C7    C8    N1
>    C4    N1    C5    C6
>
>
>
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>  
>
You are using XXX in the rtp file and YYY in pdb... put they with the 
same name... and it will work fine.

[]'s

-- 
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - Sa~o Carlos - Brasil