On 4/19/20 3:47 PM, Paolo Costa wrote:
Hi Justin,
I could fix the issue.
Thanks again for your help.
And in the spirit of helping others that use this mailing list, what
exactly was the problem and how did you solve it?
-Justin
Paolo
Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul <jalem...@vt.edu> ha
scritto:
On 4/17/20 5:25 PM, Paolo Costa wrote:
Hi Justin,
thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my
stannate.pdb and also to stannate.rtp. But still I get the error.
Here the output file of from pdb2gmx:
Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b
Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b
Reading stannate.pdb...
WARNING: all CONECT records are ignored
Read 'stannate', 7 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 7 atoms
chain #res #atoms
1 ' ' 1 7
All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp
Atomtype 68
Reading residue database... (amber99)
Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp
Residue 94
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp
Residue 110
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp
Residue 126
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp
Residue 127
Sorting it all out...
Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb
Opening force field file
/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb
Opening force field file
/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.19#
Processing chain 1 (7 atoms, 1 residues)
Warning: Starting residue SnC0 in chain not identified as
Protein/RNA/DNA.
This chain lacks identifiers, which makes it impossible to do strict
classification of the start/end residues. Here we need to guess this
residue
should not be part of the chain and instead introduce a break, but that
will
be catastrophic if they should in fact be linked. Please check your
structure,
and add SnC to residuetypes.dat if this was not correct.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the
behavior.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program: gmx pdb2gmx, version 2018.1
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639)
Fatal error:
Residue 'SnC' not found in residue topology database
*Thanks a lot for helping!*
Without seeing the contents of the PDB file and stannate.rtp, there's
not much to go on here.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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