[gmx-users] errors while running pdb2gmx

[Rahul Karyappa]

Dear all,

    I am getting error while generating .gro and .top
files using pdb2gmx. I have defined my molecule in the .rtp file as
follows:

[ PAA ]

 [ atoms ]

     HT    H    -0.0070    1

     C1  CH3    -0.2615    1

    C2*  CH2    -0.0846    1

     C3    C     0.5812    1

     O1   OM    -1.0370    1

    HC2    H     0.0995    1

   H1C1    H     0.0990    1

   H2C1    H     0.1411    1

     O2   O    -0.5020    1

     HH    H    -0.0070    1

  [ bonds ]

     HT   C1

   H1C1   C1    

   H2C1   C1

     C1  C2*

     HH  C2*

    HC2  C2*

    C2* 
C3                     

     C3   O2

     C3   O1


But when I run pdb2gmx it gives following warnings:

WARNING: atom HH is missing in residue PAA 41 in the pdb file

         You might need to add atom HH to the hydrogen database of residue PAA

         in the file ff???.hdb (see the manual)

WARNING: atom HT is missing in residue PAA 42 in the pdb file

         You might need to add atom HT to the hydrogen database of residue PAA

         in the file ff???.hdb (see the manual)

WARNING: atom O1 is missing in residue PAA 42 in the pdb file

WARNING: atom O1 is missing in residue PAA 42 in the pdb file

WARNING: atom HH is missing in residue PAA 42 in the pdb file

         You might need to add atom HH to the hydrogen database of residue PAA

         in the file ff???.hdb (see the manual)

WARNING: atom HT is missing in residue PAA 43 in the pdb file

         You might need to add atom HT to the hydrogen database of residue PAA

         in the file ff???.hdb (see the manual)

WARNING: atom O1 is missing in residue PAA 43 in the pdb file

WARNING: atom O1 is missing in residue PAA 43 in the pdb file

continued......


When I run the command--

pdb2gmx -f ....pdb -o ...gro -p ...top -ter -missing


it generates the .gro and .top files but in both the files it takes
only one oxygen and that also just O. What may be the problem?

Thanking you in advance.


Rahul Karyappa

NCL, Pune





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