On 2012-12-08 03:20:54AM -0800, James Starlight wrote:
1- on what assumptions that blocks were generated ?
This appears to be a swissparm-specific question. I don't know what
algorithms it uses to match what are essentially pharmacophores in the new
molecule with the common individual blocks it finds.
2- Why charge in [ atomtypes ] (zero) differes from the charges in
Because gromacs ignores charges in [atomtypes], so the easiest thing is to
just assign all zeros to that column.
the topology of the same groups? how I can check correctness of charge
distribution in such itp files ?
Compare to analogous molecules and see if there are published charges.
You can also use the building blocks and manually assign charges and see
what
you end up with as well. To be totally rigorous, parameterize the structure
using a quantum chemistry package and compare the ab initio charge
distributions to the ones assigned by SwissParm (or by hand).
3- What is sigma and epsilon in the [ atomtypes ] ? :)
LJ interactions in sigma-epsilon form. See gromacs manual section 4.1.1
4- Have anybody else used Swiss param for modeling protein-ligands
systems? Might it be used with the charmm36 set ?
CHARMM has its own generalized forcefield (CGenFF) for ligands and other
molecules, although charmm36 may have cAMP in their nucleotides section...
You can try to also build it using adenine, ribose, and add phosphate.
CGenFF and C36 are interoperable for intermolecular interactions, so if
using CGenFF to paramterize cAMP you would use ParamChem to assign charges
and then convert and add the CGenFF forcefield parameters (from the gromacs
contributions website) to C36. There are mailing list archives that show
you the script to use to do the CGenFF conversion.
James
2012/12/7, Justin Lemkul <jalem...@vt.edu>:
On 12/7/12 2:21 PM, James Starlight wrote:
Justin,
with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2
rvdw=1.2
rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp
NOTE 1 [file ./mdps/em.mdp]:
For energy conservation with switch/shift potentials, rlist should
be
0.1
to 0.3 nm larger than rvdw.
NOTE 2 [file ./mdps/em.mdp]:
The sum of the two largest charge group radii (0.078024) is larger
than
rlist (1.200000) - rvdw (1.200000)
As I recall, there is a small bug where grompp ignores rlistlong when
printing
this message. The simulation will be fine.
-Justin
Should I increase Rlist to the 1.4 ( as well as rcoulomb to the same
value because of PME) ?
2012/12/7, Justin Lemkul <jalem...@vt.edu>:
On 12/7/12 1:19 PM, James Starlight wrote:
Justin,
following to your advise I've tried to use charmm 27 ff for
simulation
of my protein-cGMP complex ( ligand was parametrized by Swiss Param
server).
Could you provide me with the cut-offs for vdw as well as
electrostatics suitable for simulation in charmm27 and 36 force
fields?
http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html
Does anybody know another servers for parametrization of the ligands
for charmm simulation in gromacs?
If Google can't find it, it probably doesn't exist.
-Justin
2012/12/7, Justin Lemkul <jalem...@vt.edu>:
On 12/7/12 11:42 AM, James Starlight wrote:
Justin,
ligand-only simulation in vacuum have been finished with the same
errors
:)
Step 19200, time 38.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025443, max 0.140660 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 52.2 0.1033 0.0985 0.1000
1 3 90.1 0.1168 0.1141 0.1000
Step 19200, time 38.4 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.025376, max 0.140474 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 52.0 0.1033 0.0988 0.1000
1 3 90.0 0.1168 0.1140 0.1000
step 19200, will finish Sat Dec 8 04:10:49 2012
Step 19201, time 38.402 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052715, max 0.293316 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 49.3 0.0988 0.0993 0.1000
1 3 90.0 0.1140 0.1293 0.1000
Step 19201, time 38.402 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.052900, max 0.294281 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 49.6 0.0988 0.0989 0.1000
1 3 90.0 0.1140 0.1294 0.1000
Step 19202, time 38.404 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.035783, max 0.198482 (between atoms 1 and 3)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 33.3 0.0989 0.0984 0.1000
1 3 89.9 0.1294 0.1198 0.1000
-------------------------------------------------------
Program mdrun, VERSION 4.5.4
Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176
Fatal error:
Too many LINCS warnings (1000)
ITs intresting that the same files (like step-1c_n11.pdb) have
been
produced already during CG minimisation phase but the system have
not
been crashed. So I suppoe that the problem is in geometry of the
If you get errors in the minimization, that should indicate that
either
the
topology or configuration is flawed.
mollecule. The direct comparison of the bonds and angles with the
rtp
(DGUA) is non trivial again because of differs in the file formats
representation :)
Most troubleshooting is not easy. You can also create a topology
for
DGUA
from
just about any DNA structure and compare its .top against your cGMP
topology.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
