madhumita das wrote:
Thanks Justin,
I must inform you that my pdb file has a modified cysteine residue
having a mercury atom attached to the sulphur atom next to the residue
having the atom 2700. Is the murcury atom creating any problem? I want
Probably. Parameterizing such a species properly is not trivial, if it can even
be done in a non-polarizable MM force field.
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species
to also know can I use amber forcefield in GROMACS for pdb files of lipid?
Lipids probably aren't built in, but could potentially be added if you provide
the proper parameters. CHARMM is probably a better choice. CHARMM27 is built
into Gromacs already, and CHARMM36 is available as a download from the website.
-Justin
On Tue, Nov 8, 2011 at 5:56 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
madhumita das wrote:
Hi GROMACS users,
i am in the midst of simulating a protein in water. I have
modified a residue in my pdb file at position 182, using
amber and then acpype.py. But after running the energy
minimization step,using em.mdp file generated from acpype ,
following error comes.
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 5000
Step= 17, Dmax= 1.5e-06 nm, Epot= 9.89827e+17 Fmax=
inf, atom= 2700
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 9.8982703e+17
Maximum force = inf on atom 2700
Norm of force = 1.7474532e+19
An infinite force suggests severe atomic overlap. Check the
starting structure, paying close attention to atom 2700 and its
surrounding environment.
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
<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 [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
