[gmx-users] Aminoacids.hdb problem

[Justin A. Lemkul]

Alberto Arrigoni wrote:
> *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
> *

You have specified that there are 4 lines to be read for SEP (first line of the 
entry), but only 3 follow it.  This will raise the fatal error, because the file 
format is now broken.

-Justin

> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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