Hello,
I am also having some difficulty using these parameter files. After reading
some old posts I copied the older param*.dat file with the following to the
bottom of my frcmod file:
NO 1.8240 0.1700 OPLS
NP 1.8240 0.1700 OPLS
CX 1.9080 0.0860 Spellmeyer
This is my input:
-------------
source leaprc.ff14SB
hemeparam = ~/MD/DosS-GAFA/heme_uni.frcmod
loadAmberPrep ~MD/DosS-GAFA/heme_uni.in
DosS = loadpdb 2W3E_outH2.pdb
setBox DosS vdw
sovateOct DosS TIP3BOX 10.
addIons DosS Na+ 8
savepdb DosS DosS_orig.pdb
saveamberparm DosS DosS.top DosS.crd
---------
But I receive the following error at the very end for all atoms in the heme:
FATAL: Atom .R<HIE 16>.A<HD1 18> does not have a type.
FATAL: Atom .R<HEM 149>.A<CAA 1> does not have a type.
etc….
The parameters are not written. Somehow I need to enter the types for each
atom with charge I think. Any help would be appreciated.
-Yarrow
On Wed, Oct 29, 2014 at 12:44 PM, Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Another thing is about editing the molecule in xleap.
> It seems xleap will treat the name molecule name in prep file as standard.
>
> For example, in the heme_all.in file, we can check the molecule name in
> the line:
> "HEM INT 0", HEM is the molecule name. So when you try to edit that
> molecule in xleap,
> You should use "edit HEM" command.
>
> HTH,
> Pengfei
>
> On Oct 29, 2014, at 3:35 PM, Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
> > Hi Kevin,
> >
> > It seems that you are using the all atom parameters of heme with the
> ff03-united-atom force field.
> > There is also a united atom version of the heme parameters in that
> website.
> > It would be better for you to use that one.
> >
> > I checked the heme parameter files online, it seems they have a old
> fashion style which is different
> > from the prep file nowadays use. "no charges read on…" this error may
> comes from that reason.
> > You can manually change the file from old style to the new one.
> >
> > Here is an example with the new style:
> > http://ambermd.org/antechamber/EFZ_sybyl_resp_gaff.prepc
> >
> > The mainly difference is the place of the charge information.
> >
> > Feel free to ask if you have other questions.
> >
> > HTH,
> > Pengfei
> >
> > On Oct 29, 2014, at 1:21 PM, Kevin Murphy <km6.pdx.edu> wrote:
> >
> >> Hi,
> >>
> >> I'm new to the AMBER field. I'm attempting the dynamic simulation of a
> >> drug's interaction with heme in solution. I'm trying to use the
> >> parameterized heme as available here:
> >> http://www.pharmacy.manchester.ac.uk/bryce/amber/.
> >>
> >> The following is my input:
> >>
> >>> source leaprc.ff03ua
> >>>> (parameters and libraries are successfully loaded)
> >>> loadamberparams "~/frcmod.hemall"
> >>>> Loading parameters: ~/frcmod.hemall
> >>>> Reading force field modification type file (frcmod)
> >>>> Reading title:
> >>>> Heme parameters
> >>> heme = loadamberprep "~/heme_all.in"
> >>>> Loading Prep file: ~/heme_all.in
> >>>> (no charges read on atoms lines in Heme residue ALL ATOM, Yves
> >> names, Bayly-modified)
> >>
> >> When I attempt to visualize, via "edit heme", I get ...
> >>
> >> Creating a new, empty UNIT "heme"
> >>
> >> ... and an empty visualization window.
> >>
> >> This is where I'm stuck.
> >>
> >> Thank you in advance for any help you can offer!
> >>
> >> Kevin Murphy
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
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Received on Wed Oct 29 2014 - 18:00:02 PDT
