[gmx-users] errors while running pdb2gmx

[Sanjay Nilapwar]

check this manual, this will answer most of your basic question.
This manual gives a step by step guide for many bsic tasks in gromacs

http://davapc1.bioch.dundee.ac.uk/programs/prodrg/gmx.pdf
-- 
Sanjay Nilapwar
Laboratory of molecular biophysics
department Of Biochemistry and Molecular Biology
University College Lonodon,
Gower street, London
WC1E 6BT
Tel:- 0207 679 2212


Quoting Rahul Karyappa <r.karyappa at ncl.res.in>:

> 
> 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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