Dear Moitrayee,
Many problems...
- All the hydrogens atoms are not present in your molecule; you first
need to add these (4) hydrogens; you could either use xLEaP or R.E.D.
Server:
See
http://q4md-forcefieldtools.org/REDS/faq.php#20
I do not understand how you can end up with atomic charge values in
this mol2 (output) file without all the hydrogen atoms in the P2N
input file...
- The residue name is not correct in your P2N file; May-be Ante_R.E.D.
2.0 does not correct this problem; our new R.E.D. version does.
Correct that manually; i.e. replace the column '2' by 'CIT' for
instance.
- Chemical equivalencing is correct in this P2N file; Indeed, here the
two CH2-COO(-) should be equivalent; this means they should bear the
same name two by two (2 CH2 groups equivalent and 2 COO(-) equivalent).
See
http://q4md-forcefieldtools.org/REDS/popup/popanteredtopequiv.php
Our new R.E.D. version handles that even more automatically; no more
P2N files.
- The number of geometrical constraints should be kept as small as
possible; for sure if you constraint all the dihedrals of citrate you
will get the same structure than the experimental one... please read
Cieplak et al.:
http://www3.interscience.wiley.com/cgi-bin/abstract/109583237/ABSTRACT
- No need to use Antechamber here:
- & no need to convert a mol2 file into a prep file; please read:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
mol3/mol2, off, prep file formats have all the same role: to be a FF
library file format.
- atom types can be easily added in the .mol2 file (simply replace
the chemical symbol by the atom types)
See
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
& more $AMBERHOME/dat/leap/parm/parm99.dat
CT 12.01 0.878 sp3 aliphatic C
C 12.01 0.616 sp2 C carbonyl group
H1 1.008 0.135 H aliph. bond. to C with 1
electrwd. group
HO 1.008 0.135 hydroxyl group
O2 16.00 0.434 carboxyl and phosphate group oxygen
OH 16.00 0.465 oxygen in hydroxyl group
O2 16.00 0.434 carboxyl and phosphate group oxygen
.<TRIPOS>ATOM
1 C -0.898932 -1.107716 -0.639849 CT(**) 1 CIT -0.6640(*)
2 C11 0.124175 -0.058604 -0.153210 CT 1 CIT 1.0748
3 O 0.288277 -0.676295 1.120574 OH 1 CIT -0.6454
4 H -0.225218 -0.096106 1.683964 HO 1 CIT 0.3167
5 C10 1.354615 -0.039384 -1.034103 CT(**) 1 CIT -0.6640
6 C9 2.555128 -0.398100 -0.207257 C 1 CIT 0.8603
7 O8 3.121069 0.560707 0.344407 O2 1 CIT -0.8120
8 O7 2.917251 -1.585703 -0.258239 O2 1 CIT -0.8120
9 C6 -0.351104 1.439904 0.084007 C 1 CIT 0.7813
10 O5 -0.304156 2.223542 -0.859272 O2 1 CIT -0.8360
11 O4 -0.716263 1.660876 1.251928 O2 1 CIT -0.8360
12 C3 -2.294391 -0.800455 -0.184173 C 1 CIT 0.8603
13 O2 -2.914347 -0.237493 -1.108215 O2 1 CIT -0.8120
14 O1 -2.730798 -1.210354 0.899260 O2(!) 1 CIT -0.8120
(*) re-derive the atomic charge values with hydrogen atoms...
(**) hydrogen atoms of the methylene groups are missing; they should
bear the H1 atom type...
(!) our new R.E.D. version performs atom typing automatically...
If I dare (no offense): better understanding what one does instead of
using programs like black boxes without understanding what one does &
why...
regards, Francois
> I am using angle constraints on the citrate anion (-3) based on the
> X-ray data.
> I have attached the P2N file and the .mol2 file. After optimization, I a
> conformation very similar to the experimental conformation. It would
> be great if
> you take a quick look through them and let me know if I am making some
> obvious/conceptual mistake.
>
> Also I am using antechamber to generate the prep and frcmod file for the ion
> using the following command:
>
> antechamber -i *.mol2 -fi mol2 -o *.prep -fo prepi -nc -3 -j 5
>> Dear Moitrayee,
>>
>>> We do have an electron density in the crystal structure to which the
>>> citrate was
>>> modeled. But I am not sure what sort of experimental data you are
>>> referring to.
>>> It would be immensely helpful if you please elaborate a little
>>> more so that I
> can speak to my experimental collaborator on this issue.
>>
>> I would simply check that the structure obtained after geometry
>> optimization is 'similar' to the experimental one. If not, a
>> variation of the
> whole molecule approach (described in the previous email) could be to use
> dihedral constraint(s) (a minimum number of constraints) to match the
> experimental conformation.
>>
>> You could use R.E.D. Server to perform geometry optimization with dihedral
> constraints from a P2N file;
>> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#CONSTRAINT
>>
>> If you do so, please select Gaussian version 2003 because the format of
> constraints has changed in Gaussian 09 C.01.
>>
>> regards, Francois
>>
>>
>>>>> I am performing a MD for which I would require citrate ion (-3)
>>>>> parameters. It
>>>>> would great if someone could help me with finding if there are published
> citrate
>>>>> ion parameters. I have searched the AMBER archive but did not get them.
>>>> Citrate is a complex case; this is small molecule with 3 negative
>>>> charges...
> If you decide to derive charges for the whole molecule, the
>>>> conformation obtained after geometry optimization is unlikely to be
> representative of what you want...
>>>> If you decide to follow the building block approach (see
>>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17) the
>>>> constraints
> used during charge derivation are likely to strongly affect the fit...
>>>> Do you have experimental data about citrate that could be used to
>>>> guide the
> charge derivation procedure?
>>>> regards, Francois
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Received on Mon Jan 21 2013 - 01:00:02 PST
