OK, I will add those. I've also added a new setting in Jmol 11.7.7:
set atomTypes "abcd=>C;efgh=>H"
this setting allows atom types in MOL2 file formats (5th field) to define
the element associated with that atom type. Not necessary in general, but
for future changes in the force fields, introduction of new forcefields, or
user-defined atom types, this allows complete flexibility in that regard.
Bob
On Fri, Oct 31, 2008 at 11:39 AM, FyD <[EMAIL PROTECTED]> wrote:
> Dear Bob,
>
> H1 is not listed as an AMBER atom type in that reference I used. Nor H4 H5
>> HP
>>
>> OK, so I've added those from the JACS paper.
>> See http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
>>
>> Those pink H atoms should be gone.
>>
>
> Thanks. Few points:
>
> - Below, you will find the listing of the FF atom types available for AMBER
> & GLYCAM FF in the AMBER10 distribution...
>
> - I think you did not add the "CG" & "CY" FF atom types from Glycam. In
> fact, you can consider GLYCAM + AMBER FF as a single "AMBER" FF.
>
> - I think a problem will show up with Jmol when a user will define its own
> FF atom types, i.e. when a users create a new FF atom types: I think Jmol
> will color it in pink each time...
>
> best regards, Francois
>
>
> AMBER FF:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> C 12.01 0.616 ! sp2 C carbonyl group
> CA 12.01 0.360 sp2 C pure aromatic (benzene)
> CB 12.01 0.360 sp2 aromatic C, 5&6 membered ring
> junction
> CC 12.01 0.360 sp2 aromatic C, 5 memb. ring HIS
> CD 12.01 0.360 sp2 C atom in the middle of: C=CD-CD=C
> CK 12.01 0.360 sp2 C 5 memb.ring in purines
> CM 12.01 0.360 sp2 C pyrimidines in pos. 5 & 6
> CN 12.01 0.360 sp2 C aromatic 5&6 memb.ring
> junct.(TRP)
> CQ 12.01 0.360 sp2 C in 5 mem.ring of purines between
> 2 N
> CR 12.01 0.360 sp2 arom as CQ but in HIS
> CT 12.01 0.878 sp3 aliphatic C
> CV 12.01 0.360 sp2 arom. 5 memb.ring w/1 N and 1 H
> (HIS)
> CW 12.01 0.360 sp2 arom. 5 memb.ring w/1 N-H and 1 H
> (HIS)
> C* 12.01 0.360 sp2 arom. 5 memb.ring w/1 subst. (TRP)
> CY 12.01 0.360 nitrile C (Howard et
> al.JCC,16,243,1995)
> CZ 12.01 0.360 sp C (Howard et al.JCC,16,243,1995)
> C0 40.08 calcium
> H 1.008 0.161 H bonded to nitrogen atoms
> HC 1.008 0.135 H aliph. bond. to C without
> electrwd.group
> H1 1.008 0.135 H aliph. bond. to C with 1 electrwd.
> group
> H2 1.008 0.135 H aliph. bond. to C with 2
> electrwd.groups
> H3 1.008 0.135 H aliph. bond. to C with 3
> eletrwd.groups
> HA 1.008 0.167 H arom. bond. to C without elctrwd.
> groups
> H4 1.008 0.167 H arom. bond. to C with 1 electrwd.
> group
> H5 1.008 0.167 H arom.at C with 2 elctrwd. gr,+HCOO
> group
> HO 1.008 0.135 hydroxyl group
> HS 1.008 0.135 hydrogen bonded to sulphur (pol?)
> HW 1.008 0.000 H in TIP3P water
> HP 1.008 0.135 H bonded to C next to positively
> charged gr
> HZ 1.008 0.161 H bond sp C (Howard et
> al.JCC,16,243,1995)
> F 19.00 0.320 fluorine
> Cl 35.45 1.910 chlorine (Applequist)
> Br 79.90 2.880 bromine (Applequist)
> I 126.9 4.690 iodine (Applequist)
> IM 35.45 3.235 assumed to be Cl- (ion minus)
> IB 131.0 'big ion w/ waters' for vacuum (Na+,
> 6H2O)
> MG 24.305 0.120 magnesium
> N 14.01 0.530 sp2 nitrogen in amide groups
> NA 14.01 0.530 sp2 N in 5 memb.ring w/H atom (HIS)
> NB 14.01 0.530 sp2 N in 5 memb.ring w/LP
> (HIS,ADE,GUA)
> NC 14.01 0.530 sp2 N in 6 memb.ring w/LP (ADE,GUA)
> N2 14.01 0.530 sp2 N in amino groups
> N3 14.01 0.530 sp3 N for charged amino groups (Lys,
> etc)
> NT 14.01 0.530 sp3 N for amino groups amino groups
> N* 14.01 0.530 sp2 N
> NY 14.01 0.530 nitrile N (Howard et
> al.JCC,16,243,1995)
> O 16.00 0.434 carbonyl group oxygen
> O2 16.00 0.434 carboxyl and phosphate group oxygen
> OW 16.00 0.000 oxygen in TIP3P water
> OH 16.00 0.465 oxygen in hydroxyl group
> OS 16.00 0.465 ether and ester oxygen
> P 30.97 1.538
> phosphate,pol:JACS,112,8543,90,K.J.Miller
> S 32.06 2.900 S in disulfide
> linkage,pol:JPC,102,2399,98
> SH 32.06 2.900 S in cystine
> CU 63.55 copper
> FE 55.00 iron
> Li 6.94 0.029 lithium, ions
> pol:J.PhysC,11,1541,(1978)
> IP 22.99 0.250 assumed to be Na+ (ion plus)
> Na 22.99 0.250 Na+, ions pol:J.PhysC,11,1541,(1978)
> K 39.10 1.060 potassium
> Rb 85.47 rubidium
> Cs 132.91 cesium
> Zn 65.4 Zn2+
> LP 3.00 0.000 lone pair
>
> GLYCAM FF:
> GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004
> CG 12.01 ! sp3 C aliphatic
> CT 12.01 sp3 C aliphatic
> CY 12.01 sp3 C aliphatic
> C 12.01 sp2 C carbonyl group
> H 1.008 H Bonded to nitrogen atoms
> H1 1.008 H aliph. bond. to C with 1 electrwd.
> groups
> H2 1.008 H aliph. bond. to C with 2 electrwd.
> groups
> HC 1.008 H aliph. bond. to C without electrwd.
> groups
> HO 1.008 H hydroxyl group
> HW 1.008 H TIP3P water
> N 14.01 sp2 N amide group
> O 16.00 O carbonyl group
> O2 16.00 O carboxyl group
> OH 16.00 O hydroxyl group
> OS 16.00 O ether
> OW 16.00 O TIP3P water
>
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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