[gmx-users] RE: missing atom

[Justin Lemkul]

On 1/11/13 4:55 AM, Subramaniam Boopathi wrote:
> Hello All
>
>
>                     I have created a nwe residue "NIC" in AMBER 03
> Forcrfield and I have added corresponding data to the aminoacid.rtp  In the
> aminoacid.rtp,  I have added all atoms topology information then I type the
> command
>
>
>                           * ./pdb2gmx_d -f abnic.pdb -o abnic.gro -p
> abnic.top -ignh
> *
>
> but it told me some atoms are missing
>
>
>                   atom HAQ is missing in residue NIC 8 in the pdb file
>           You might need to add atom HAQ to the hydrogen database of
> building block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HB1 is missing in residue NIC 8 in the pdb file
>           You might need to add atom HB1 to the hydrogen database of
> building block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HB2 is missing in residue NIC 8 in the pdb file
>           You might need to add atom HB2 to the hydrogen database of
> building block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HG1 is missing in residue NIC 8 in the pdb file
>           You might need to add atom HG1 to the hydrogen database of
> building block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HG2 is missing in residue NIC 8 in the pdb file
>           You might need to add atom HG2 to the hydrogen database of
> building block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HD1 is missing in residue NIC 8 in the pdb file
>           You might need to add atom HD1 to the hydrogen database of
> building block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HD2 is missing in residue NIC 8 in the pdb file
>           You might need to add atom HD2 to the hydrogen database of
> building block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HE1 is missing in residue NIC 8 in the pdb file
>           You might need to add atom HE1 to the hydrogen database of
> building block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HE2 is missing in residue NIC 8 in the pdb file
>           You might need to add atom HE2 to the hydrogen database of
> building block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HE3 is missing in residue NIC 8 in the pdb file
>           You might need to add atom HE3 to the hydrogen database of
> building block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HT is missing in residue NIC 8 in the pdb file
>           You might need to add atom HT to the hydrogen database of building
> block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HV is missing in residue NIC 8 in the pdb file
>           You might need to add atom HV to the hydrogen database of building
> block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HN is missing in residue NIC 8 in the pdb file
>           You might need to add atom HN to the hydrogen database of building
> block NIC
>           in the file aminoacids.hdb (see the manual)
>
>
> WARNING: atom HM is missing in residue NIC 8 in the pdb file
>           You might need to add atom HM to the hydrogen database of building
> block NIC
>           in the file aminoacids.hdb (see the manual)
>
>    can yopu please help me to overcome this problem. I am a buddy stage to
> learn GROMACS.
>

You need a suitable .hdb entry to reconstruct missing hydrogen atoms.  See the 
manual and refer to existing examples in aminoacids.hdb.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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