HEM.mol2
I confused as to how to get the atom types into the heme_uni.in file. I
have the following MOl2 file for the heme with atom types (below). Sorry
about this naive question.
-Yarrow
HEM.mol2
# Shahrokh,K; Orendt,A; Yost, G.S; and Cheatham III, T.E. Jour Comp Chem
(2011)
# Ferric penta-coordinate high-spin (IC6) heme coordinates and atomic
charges
.<TRIPOS>MOLECULE
HEM-IC6
73 80 1 0 1
SMALL
USER_CHARGES
.<TRIPOS>ATOM
1 NC 2.946000 -0.972000 -0.732000 nc 1 HEM 0.0066
****
2 C1C 4.282000 -0.756000 -0.518000 cc 1 HEM -0.0192
****
3 C4C 2.796000 -2.285000 -1.056000 cc 1 HEM -0.0193
****
4 C2C 5.025000 -1.989000 -0.700000 cc 1 HEM 0.0114
****
5 C3C 4.097000 -2.957000 -1.046000 cc 1 HEM -0.0357
****
6 CHD 1.576000 -2.892000 -1.394000 cg 1 HEM -0.1482
****
7 HHD 1.613000 -3.945000 -1.655000 ha 1 HEM 0.1094
****
8 C1D 0.319000 -2.288000 -1.482000 cd 1 HEM 0.0095
****
9 ND 0.056000 -0.976000 -1.204000 nd 1 HEM -0.2714
****
On Wed, Oct 29, 2014 at 5:34 PM, Yarrow Madrona <Acacia.Madrona.ucsf.edu>
wrote:
> 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
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Oct 29 2014 - 18:00:03 PDT
