Urszula,
> I attached you my mol2 file, please propose me the atom types,
Yes you inverted CR & CW...
see the mol2 files:
1 N5 -0.677753 0.775716 -0.816960 N 1 THZ -0.5570
2 H5 -0.047858 0.884178 -1.583803 H 1 THZ 0.3305
3 C6 -0.763415 -0.575273 -0.283832 CT 1 THZ 0.1240
4 H6 -0.531884 -1.215582 -1.126640 H1 1 THZ 0.0084
5 C -2.187031 -0.969683 0.125740 C 1 THZ 0.6667
6 O -2.393882 -1.680460 1.072762 O 1 THZ -0.5901
7 CB 0.257776 -0.908432 0.813639 CT 1 THZ -0.0446
8 HB2 0.055792 -0.350584 1.718940 HC 1 THZ 0.0319
9 H83 0.143837 -1.955888 1.063840 HC 1 THZ 0.0319
10 C8 1.667541 -0.646510 0.362644 CC 1 THZ 0.2652
11 C9 2.606602 0.040432 1.033680 CW 1 THZ -0.3191
12 H9 2.516203 0.528308 1.981537 H4 1 THZ 0.2400
13 S16 4.087930 0.054545 0.145236 S 1 THZ -0.0074
14 C11 3.304933 -0.870422 -1.079144 CR 1 THZ 0.1040
15 H11 3.827580 -1.171423 -1.966315 H5 1 THZ 0.1643
16 N13 2.083892 -1.160010 -0.853022 NB 1 THZ -0.4488
the frcmod file:
----------------------------
frcmod file
MASS
BOND
CW-S 430.0 1.725 FF cst adapted from CW-NA; Eq.val. from QM
opt.geom.
CR-S 480.0 1.725 FF cst adapted from CR-NA; Eq.val. from QM
opt.geom.
ANGL
CC-CW-S 70.0 120.00 FF cst adapted from CC-CW-NA
CR-S -CW 70.0 120.00 FF cst adapted from CR-NA-CW
H4-CW-S 50.0 120.00 FF cst adapted from H4-CW-NA
H5-CR-S 50.0 120.00 FF cst adapted from H5-CR-NA
S -CR-NB 70.0 120.00 FF cst adapted from NA-CR-NB
DIHE
X -CR-S -X 2 4.70 180.0 2. adapted from X -CR-NA-X
X -CW-S -X 2 3.00 180.0 2. adapted from X -CW-NA-X
IMPROPER
NONB
-------------------------------
You might adapt the equilibrium values of the bonds & angles for your
heterocycle...
It seems to work; please triple check what I did...
regards, Francois
> ________________________________________
> Von: FyD [fyd.q4md-forcefieldtools.org]
> Gesendet: Donnerstag, 1. Dezember 2011 13:20
> An: AMBER Mailing List
> Betreff: Re: [AMBER] atom types error
>
> Dear Urszula,
>
> Simply open the parm99.dat file . $AMBERHOME/dat/leap/parm/ and:
>
> gedit $AMBERHOME/dat/leap/parm/parm99.dat &
>
> Check if the CC-CR force field parameter (bond) do exist: no
> but CC-CW does exist:
> CC-CW 518.0 1.371 JCC,7,(1986),230; HIS(epsilon)
>
> I wonder if you did not invert the CR and CW atom types in your cycle:
> look at their definition in parm99.dat
>
> then, for sure S-CW and/or S-CR does not exist ;-) you will have to
> create this FF parameter by analogy to an existing FF parameter; just
> copy/cut the FF constant in this case (this is a cycle) and take the
> equilibrium value from the QM geometry optimization.
>
> or send me your mol2 file and I will propose you atom types & a
> frcmod file...
>
> regards, Francois
>
>
>> I have still problems with adding correct FF atom types to my mol2
>> file, (attached)
>>
>> > check x
>> Checking 'x'....
>> Checking parameters for unit 'x'.
>> Checking for bond parameters.
>> Could not find bond parameter for: CC - CR
>> Could not find bond parameter for: CR - S
>> Could not find bond parameter for: S - CW
>> Could not find bond parameter for: CW - NB
>> Checking for angle parameters.
>> Could not find angle parameter: CT - CC - CR
>> Could not find angle parameter: CC - CR - H5
>> Could not find angle parameter: CC - CR - S
>> Could not find angle parameter: CC - NB - CW
>> Could not find angle parameter: CR - CC - NB
>> Could not find angle parameter: CR - S - CW
>> Could not find angle parameter: H5 - CR - S
>> Could not find angle parameter: S - CW - H4
>> Could not find angle parameter: S - CW - NB
>> Could not find angle parameter: H4 - CW - NB
>> There are missing parameters.
>> Unit is OK.
>>> quit
>>
>> this is what i am getting, I also run antechamber for the molecule
>> and changed the CR and CW to CD but it did not help much,
>>
>> Can you suggest me something here?
>>
>> /Urszula
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Received on Thu Dec 01 2011 - 06:30:04 PST
