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
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--
========================================
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
========================================
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