Hi Yarrow,
On Oct 29, 2014, at 8:46 PM, Yarrow Madrona <Acacia.Madrona.ucsf.edu> wrote:
> 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).
1 DUMM DU M 0 -1 -2 0.0000 0.0000 0.0000 0.000
2 DUMM DU M 1 0 -1 1.4490 0.0000 0.0000 0.000
3 DUMM DU M 2 1 0 1.5220 111.1000 0.0000 0.000
4 N N M 3 2 1 1.3350 116.6000 180.0000 0.000
5 HN H E 4 3 2 1.0100 119.8000 0.0000 0.000
6 CA CH M 4 3 2 1.4490 121.9000 180.0000 0.000
7 CB C2 S 6 4 3 1.5250 111.1000 60.0000 0.000
8 CG CC S 7 6 4 1.5100 115.0000 180.0000 0.000
9 ND1 NA B 8 7 6 1.3900 122.0000 180.0000 0.000
10 HND H E 9 8 7 1.0100 126.0000 0.0000 0.000
11 CE1 CP S 9 8 7 1.3200 108.0000 180.0000 0.000
12 NE2 NB B 11 9 8 1.1300 109.0000 0.0000 0.000
13 CD2 CF E 12 11 9 1.3600 110.0000 0.0000 0.000
14 FE FE S 12 11 9 2.1000 124.0000 180.0000 0.000
15 NA NP S 14 12 11 2.0800 98.0000 90.0000 0.000
For example, in above lines, you have the atom types in the third column.
You can check this webpage
http://ambermd.org/doc/prep.html
to get further information about the prep file format.
HTH,
Pengfei
> 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 Thu Oct 30 2014 - 12:30:03 PDT
