[gmx-users] Aminoacids.hdb problem

[Alberto Arrigoni]

*Dear gmx-users,
I am trying to insert a custom residue (a phosphoserine) in Gromacs using
force field Amber ff99sb-ildn.
I created a new .rtp entry named SEP like this:*

[SEP]
 [ atoms ]
     N    N           -0.49370     1
     H    H            0.30180     2
     CA   CT          -0.23800     3
     HA   H1           0.09370     4
     CB   CT           0.07820     5
     HB1  H1          -0.06020     6
     HB2  H1          -0.06020     7
     OG   OS          -0.55930     8
     PS   P            1.40000     9
     OPA  O2          -0.85000    10
     OPB  O2          -0.85000    11
     OPC  O2          -0.85000    12
     C    C            0.67310    13
     O    O           -0.58540    14
 [ bonds ]
     N     H
     N    CA
    CA    HA
    CA    CB
    CA     C
    CB   HB1
    CB   HB2
    CB    OG
    OG    PS
    PS   OPA
    PS   OPB
    PS   OPC
     C     O

*After that, I got this error:*

WARNING: atom H is missing in residue SEP 124 in the pdb file
         You might need to add atom H to the hydrogen database of building
block SEP
         in the file aminoacids.hdb (see the manual)


WARNING: atom HA is missing in residue SEP 124 in the pdb file
         You might need to add atom HA to the hydrogen database of building
block SEP
         in the file aminoacids.hdb (see the manual)


WARNING: atom HB1 is missing in residue SEP 124 in the pdb file
         You might need to add atom HB1 to the hydrogen database of
building block SEP
         in the file aminoacids.hdb (see the manual)


WARNING: atom HB2 is missing in residue SEP 124 in the pdb file
         You might need to add atom HB2 to the hydrogen database of
building block SEP
         in the file aminoacids.hdb (see the manual)


-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2top.c, line: 1449

Fatal error:
There were 4 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
*

So, I modified aminoacids.hdb adding a new entry for SEP:*

SEP     4
1       1       H       N       -C      CA
1       5       HA      CA      N       CB      C
2       4       HB      CB      CA      N
*
but when I tried to use pdb2gmx in order to create .gro and .top files I
got the following error:*
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: h_db.c, line: 174

Fatal error:
Error reading from file
/usr/local/gromacs/share/gromacs/top//amber99sb-ildn.ff/aminoacids.hdb
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
_______________________________

*This is not making any sense to me, since the file is still there, and the
only change was the new SEP entry...*
I appreciate any help you could give!
Best regards

Alberto
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