onetwo wrote:
Hello Justin,
Thanks for the reply.
Sorry to say but I chose the GROMOS force field as for that topology of
the ligands could be prepared by PRODRG and I followed tutorials
available for Gromacs and most of them used GROMOS forcefield and for
starting, parameters used in the tutorials helped me to create .mdp file
for my problem.
I may be wrong in such choice of forefield.
There's a lesson to be learned here. There is no substitute for doing your
homework - reading about all the force fields, their underlying theory and
assumptions, and work that demonstrates their advantages and limitations. You
must always defend your choices to a critical audience (i.e., reviewers) and "I
saw it in a tutorial" is never going to be good enough :)
I tried yesterday installing Amber utility for gromacs but when I tried
to generate topology of protein with Mangnese, It was giving same error
as Mn is not present in its database as also mentioned in the following
website http://ffamber.cnsm.csulb.edu/.
A tip: when posting error messages, quote the command you are using and the
actual error message you receive. I have no idea what you're talking about
here. True, manganese is not included in the ffamber ports, that much is
already stated. What you should try at this point is a simple web search.
Google is your friend. The first search result for "amber manganese" (without
the quotes) is probably useful...
-Justin
Any help ?
I am really thankful to you for ur time and patience.
Regards
onetwo wrote:
> Thanks Justin for the help,
>
> I have Manganese in my protein with other two ligands at the active site.
> I am using GROMOS96 43a1 force field.
>
> Mangnese may have topology similar to Magnesium 2+, What I found is that
Assuming a transition metal "may" be similar to another species is
probably a pretty poor assumption. Prepare for lots of criticism if you
proceed with that thought.
> I need to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should
I calculate the nonbond_params for ffG43a1nb.itp.
>
Refer to the other GROMOS papers for how they derive parameters for
small molecules. I've never seen a demonstration of transition metal
parameterization under these force fields, though. Perhaps you should be
using an AMBER force field that contains Mn2+. Any particular reason you
think you need GROMOS?
> For both the other two ligands which contains phosphate and enol
groups, I was able to create topology using PRODRG server.
Please pay careful attention to the second paragraph here:
http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/PRODRG#Tips
-Justin
>
> Regards
>
> onetwo wrote:
> > Hello All,
> >
> > I am new in this field, and I want to do simulation study on one of
the protein conatining a metal ion and study its ability to form
co-oridnation bond with other ligand, which is not defined in GROMOS
force field which I have tried. If this choice of force field is correct
for such type of study ?
> >
> > I have read Gromacs Manual Chapter 5, also I am following this
gromacs mailing list for quite some time to get a help on how to include
a new metal ion or a new ligand in their simulation and they have been
refered to refer to the
http://www.gromacs.org/Documentation/How-tos/Parameterization,
> >
> > but in this its not mentioned that how to actually do parameterization
> >
> > neither in manual it has been told on how to generate it ( due
apologies,,I know, I may be wrong )
> >
>
> The manual will not cover every possible topic. Parameterization is
described in the primary literature for the force field you wish you
use. "GROMOS" is not very specific - there are numerous parameter sets
within this class of force field.
>
> > and it is more difficult for a person like me who doesnt have much
knowledge in this field, so if someone can please help me guiding how to
do parameterisation, I know this is not a trivial task, but still help
in this regard may help many other fellow users besides me.
>
> Aside from telling you to read all the literature you can, there's
not much more help anyone can do to help you. You haven't described very
well what your system is. What kind of functional groups are in your
ligand? If the functional groups are shared with existing parameters,
then you'll have a rather easy time constructing a topology. What type
of metal ion is it? If you're dealing with a transition metal, using a
standard MM force field may not work very well. Note the "Exotic
Species" heading on the page you quoted above.
>
> -Justin
>
> > Thanks in advance
> >
> >
>
> -- ========================================
>
> 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 gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
>
>
-- ========================================
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 gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Go to Previous message | Go to Next message | Back to Messages
ASCII (ASCII)Greek (ISO-8859-7)Greek (Windows-1253)Latin-10
(ISO-8859-16)Latin-3 (ISO-8859-3)Latin-6 (ISO-8859-10)Latin-7
(ISO-8859-13)Latin-8 (ISO-8859-14)Latin-9 (ISO-8859-15)W. European
(850)W. European (CP858)W. European (HPROMAN8)W. European (MACROMAN8)W.
European (Windows-1252)Armenia (ARMSCII-8)Baltic Rim (ISO-8859-4)Baltic
Rim (WINDOWS-1257)Cyrillic (866)Cyrillic (ISO-8859-5)Cyrillic
(KOI8-R)Cyrillic (KOI8-RU)Cyrillic (KOI8-T)Cyrillic (KOI8-U)Cyrillic
(WINDOWS-1251)Latin-2 (852)Latin-2 (ISO-8859-2)Latin-2
(WINDOWS-1250)Turkish (ISO-8859-9)Turkish (WINDOWS-1254)Arabic
(ISO-8859-6,ASMO-708)Arabic (WINDOWS-1256)Hebrew (856)Hebrew (862)Hebrew
(WINDOWS-1255)Chinese Simplified (GB-2312-80)Chinese Simplified
(GB18030)Chinese Simplified (HZ-GB-2312)Chinese Simplified
(ISO-2022-CN)Chinese Simplified (WINDOWS-936)Chinese Trad.-Hong Kong
(BIG5-HKSCS)Chinese Traditional (BIG5)Chinese Traditional
(EUC-TW)Japanese (SHIFT_JIS)Japanese (EUC-JP)Japanese
(ISO-2022-JP)Korean (ISO-2022-KR)Korean (EUC-KR)Thai (TIS-620-2533)Thai
(WINDOWS-874)Vietnamese (TCVN-5712)Vietnamese (VISCII)Vietnamese
(WINDOWS-1258)Unicode (UTF-7)Unicode (UTF-8)Unicode (UTF-16)Unicode (UTF-32)
| Full Headers
Reply Reply All Forward Forward
Mail Search
WelcomeInboxNewFoldersMail Options
<http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline....@middle?>
--
========================================
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 gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
