Lara Bunte wrote:
Hello
I got the following error (my command is pdb2gmx -f coord.pdb -water
tip3p ) :
Warning: Number of atoms in coord.pdb is 0
Software inconsistency error:
Trying to deduce atomnumbers when no pdb information is present
My pdb file has the following structure
HEADER my molecules name
ATOM 1 5.33618975678115 -0.07916062770658
1.39429663262701 n
ATOM 2 6.73371782109540 -2.15676333272371
0.62908982963763 c
ATOM 3 9.03483733311025 -2.20332618463802
0.65509246122614 o
ATOM 4 5.38645647191591 -4.30702600755030
-0.22693721129824 n
ATOM 5 2.79934580695015 -4.52186897159807
-0.44786509349390 c
ATOM 6 1.68306568299327 -6.40460311779204
-1.24068079528474 o
ATOM 7 1.48545702127742 -2.26124629061096
0.37342878111953 c
The numbers are cartesian coordinates in Bohrs
The file does not follow standard PDB format, which is required by all Gromacs
programs to function properly.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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