[gmx-users] phosphotyrosine

farial tavakoli farial.tavakoli at ymail.com
Mon Jan 1 13:08:59 CET 2018

Dear gmx users
I used CHARMM36 ff to generate topology for my complex which has 2 phosphotyrosines. when I issed gmx pdb2gmx command , I faced to this error:
Fatal error:
Residue 1 named PRO of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
I couldnt understand what it meant . my protein residue 1 is Gly and peptide residue 1 is Thr. there is no residue Pro in position 1 in both molecules. In addition, I checked merged.rtp file of CHARMM36 ff to compare pro residue in it with the input file , but everything sound be ok.  I dont know , what should I do. I would really appreciate it if anybody helps me
best Farial

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