[gmx-users] pdb2gmx vsites error reading atom name
Sotirios Dionysios I. Papadatos
si.papadatos at edu.cut.ac.cy
Tue Dec 6 18:37:37 CET 2016
Maybe you are trying to simulate a molecule that is not mentioned in the aminoacids.rtp on the force field of your choice or more probably the atom that is mentioned on the error report has a different name than the the one provided on the pdb file.
My advice is to check on the ff directory > aminoacids.rtp the molecule name and see the atom names that it needs.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Vasiliu Tudor <vasiliutudor_ro at yahoo.com>
Sent: Tuesday, December 6, 2016 3:29:19 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] pdb2gmx vsites error reading atom name
Hello I was wondering if someone has any idee as to what is happening with my .gro file.These are the first 3 atoms in my .gro file
1URE 10C 1 0.570 0.517 0.272
1URE 11C 2 0.555 0.365 0.285
1URE 12C 3 0.505 0.592 0.388now these are the first 3 atoms in the .rtp file[ URE ]
[ atoms ]
10C CG311 0.045 1
11C CG321 0.037 1
12C CG321 0.037 1
when I run the pdb2gmx command: echo '1' | pdb2gmx -f Uree.1.gro -vsite hydrogens -water tip3p -o vsUree.0.gro -p Uree.topI get the following error : Fatal error:
Atom 0C1 in residue URE 1 was not found in rtp entry URE with 43 atoms
while sorting atoms.
can someone pls tell my why gromacs see's the first atom as 0C1 instead of 10C? P.S. If I load the .gro file in VMD the name of the first atom is 10C and if I change in the .rtp 10C to 0C1 it works and asks for atom 1C1 and so on
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