shahrbanoo karbalaee wrote:
Dear justin
Hi,
In my simulation with ff53a5 when I do this command pdb2gmx -f
name.pdb -ter -ignh -water spce .I find this error .C-terminus: None
Now there are 14 residues with 138 atoms
Making bonds...
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Number of bonds was 142, now 139
Generating angles, dihedrals and pairs...
Before cleaning: 210 pairs
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.2
Source code file: pgutil.c, line: 87
Fatal error:
Atom H not found in residue 14 while adding improper
how can resolve this problem?
I'm assuming you're using -ter to add some sort of capping group to the
C-terminus. It seesms that there is some inconsistency between your structure
nomenclature for this atom and that which is expected by the .rtp/.tdb file.
-Justin
best regards
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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