[gmx-users] Atom X in residue YYY was not found in rtp fil
addiw7 at googlemail.com
Sat Feb 27 22:38:06 CET 2016
Dear Gromacs Experts,
I have created a new residue for which atom names in my *.pdb file are
When I run gmx pdb2gmx I get following error
Atom MCA in residue CH6 65 was not found in rtp entry CH6 with 33 atoms
while sorting atoms.
I am absolutely one hundred percent sure that I did not define atom called
There are atoms such as MCA1, MCA2, etc. in my *.rtp and other relevant
files. I think that the issue is related to the fact that in my *.pdb file,
the atom name
is now "glued" to residue name:
ATOM 478 N CH6 A 65 11.385 68.446 -10.896 1.00
ATOM 479 MCA1CH6 A 65 10.237 67.920 -10.172 1.00 14.40 C
ATOM 480 MC1 CH6 A 65 9.431 69.147 -9.749 1.00
This is part of my *.pdb file. I know that it should not be a problem,
files are read by positions, like *.gro files, but I cannot see any other
On the other hand, I have already worked with similar system and I did not
such an issue.
Could you give a hand or a tip with this one, please?
I use Gromacs 5.0.4
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