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
--
========================================
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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