Hi All,
I am trying to perform simulation of a phosphorylated protein (phos. on a
Ser residue). I am tring to use *ffG43a1p as my forcefield.
When I add a phosphate to the Ser, modify SER to SEP and run pdb2gmx it
gives me this :
***
WARNING: atom HG1 is missing in residue THR 1 in the pdb file
You might need to add atom HG1 to the hydrogen database of residue
THR
in the file ff???.hdb (see the manual)
WARNING: atom H is missing in residue SEP 2 in the pdb file
You might need to add atom H to the hydrogen database of residue
SEP
in the file ff???.hdb (see the manual)
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.1
Source code file: add_par.c, line: 221
Fatal error:
Atom NE21 not found in rtp database in residue GLN, it looks a bit like NE2
-------------------------------------------------------
*Same protein without the phosphate and OPLS forcefield does not throws any
error.I have checked my pdb file and there is no NE21 in that.
If any one has done a simulation with a phosphorylated protein using
**ffG43a1p,
then a sample pdb file would be very helpful and appreciated.*
*
Best,
*--
Ambrish Roy
Graduate Student
Bioinformatics Center
University of Kansas
2030 Becker Dr
Lawrence, KS 66047
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