[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

[vivek sharma]

Hi David,
Thanx a lot again. can you please tell me the criteria or the standards to
do such correction or can you suggest some link or tutorial for the same?
whether swiss pdb can help in such cases?

With Thanx,
Vivek



2008/8/12 David van der Spoel <spoel at xray.bmc.uu.se>

> vivek sharma wrote:
>
>> Hi There,
>>
>> I am new to molecular dynamics and GROMACS.
>> While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the
>> command....
>>
>>  pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen
>> -water spce
>>
>> I got the following in the last of error.....
>> ......
>> ......
>> ......
>> .......
>> N-terminus: NH3+
>> C-terminus: COO-
>> WARNING: atom CE2 not found in residue 270 while adding atom
>>
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: genhydro.c, line: 304
>>
>> Fatal error:
>> Atom CE2 not found in residue PHE270 while adding hydrogens
>> -------------------------------------------------------
>>  I tried the same with different force field and water models, but getting
>> the same error again and again.
>> any suggestion will be highly appreciated.
>>
>
> You have an incorrect pdb file. An atom is missing. You have to fix it
> yourself.
>
>>
>>
>> With thanx,
>> Vivek
>>
>> ------------------------------------------------------------------------
>>
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>
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