On 11/26/17 9:32 AM, MD wrote:
Thank you Mark.
Do you think if the atom types of HE, OE and SG are correct in my
merged.rtp? These are the three atoms which have name changing cause of the
inserted sulfur. I modified their atom types as well. I need to make sure
the type names are correct before I add the bond types in ffbonded.itp.
O is the carbonyl oxygen type in CHARMM, so I doubt that's a wise
choice. You may also need an entirely different sulfur atom type. Have
you assessed QM water interactions and dipole moments? Where did these
charges come from? If you haven't done so already, you need to do some
really basic validation before attempting to do anything with bonded
parameters. The dihedrals will be particularly sensitive to the quality
of LJ and charge terms.
-Justin
[ CSO ]
[ atoms ]
N NH1 -0.470 0
HN H 0.310 1
CA CT1 0.070 2
HA HB1 0.090 3
CB CT2 -0.110 4
HB1 HA2 0.090 5
HB2 HA2 0.090 6
SG S 0.6 7
OE O -0.83 8
HE1 H 0.160 9
C C 0.510 10
O O -0.510 11
[ bonds ]
CB CA
SG CB
SG OE
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
OE HE1
O C
On Thu, Nov 23, 2017 at 12:25 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
Hi,
You need to specify each bond you want, and for the types of those bonds to
have parameters available. Bonds are specified with atoms, bond types are
specified with atom types.
Mark
On Thu, 23 Nov 2017 04:22 MD <refm...@gmail.com> wrote:
Yes. You are right about the names. I wrote them by memory and they were
not printed from the terminal. I will try to edit the ffbonded.itp and
see
how it goes. Thanks!
Ming
On Wed, Nov 22, 2017 at 10:14 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/22/17 10:11 PM, MD wrote:
Justin, originally I did use SG and OE in the [bonds] and I got
complaints of "SG-OE no default bond type" "CB SG OE" no default U-B
type
and "CT1, CT2, SG, OE" no default proper dihedral gypes. Are these the
Make sure you're clear on what needs to be done, because what you've
written above is not correct and would never be printed - your dihedral
is
a mix of types and names. All parameters are assigned by type, never by
name.
parameters you mean that are missing? If so, what files do you think I
should modify to create these parameters? ffbonded.itp, merged.rtp and
residuetype.dat?
ffbonded.itp
-Justin
On Wed, Nov 22, 2017 at 10:01 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 11/22/17 9:57 PM, MD wrote:
Thanks Justin. Then do I need to create new bond of SG and OE in
ffbonded.itp? Cause I have tried adding SG and OE bond in
ffbonded.itp
and
SG and OE are atom names, not types. That's not a valid approach.
I got complaint from gromacs.. I modified the SG-OE bond from S-O
bond
and
it should work...
The [bonds] section requires atom names in order to function, so use
of
SG
and OE here is correct (your original entry used S and O, which are
atom
types and therefore not correct). If grompp subsequently complains
about
missing force field parameters when the correct bonds are written to
the
topology, then what you're attempting to do is not supported by the
force
field and you will have to either parametrize those missing
interactions
or
find parameters.
-Justin
On Wed, Nov 22, 2017 at 9:42 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 11/22/17 9:32 PM, MD wrote:
Hi gromacs folks,
I was trying to introduce sulfenic acid as modified cysteine to
the
forcefield as following. Everything went well until the "gmx mdrun
-v
-deffnm em". The only file I modified was merged.rtp since there
were
no
new bond or dihedral angles. However my sulfenic acid falls apart
(oxygen
and sulfur are far away from the protein) after mdrun. Any help or
suggestions what I should do next? I am reading the manual at the
same
time
but I thought maybe I can get some help here as well.
Thank you for your time and any advice will be appreciated.
Ming
[ CSO ]
[ atoms ]
N NH1 -0.470 0
HN H 0.310 1
CA CT1 0.070 2
HA HB1 0.090 3
CB CT2 -0.110 4
HB1 HA2 0.090 5
HB2 HA2 0.090 6
SG S 0.6 7
OE O -0.83 8
HE1 H 0.160 9
C C 0.510 10
O O -0.510 11
[ bonds ]
CB CA
S CB
S O
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
OE HE1
O C
You need a bond between SG and OE.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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