Dear Francois,
Thanks a lot for such a detailed reply and pointers about solving this problem.
I am new to this method and am being much benefited by your comments and
suggestions.
I have taken care of all the points that you had mentioned. I have added
hydrogens, I have ensured chemical equivalencing by studying the p2n file in
pymol, and used two angle constraints. I tried using fewer, but the resultant
citrate ion was becoming distorted (the CH2 groups were showing angles similar
in that of sp2, so I used constraints as seen in the structure).
Then I used the mol3 format for using in leap, I did loadmol3 and savemol3 in
xleap followed by a saveoff to generate the CIT.off file. I generate a frcmod
file using parmchk on the mol2 files. I load the files in leap using loadoff and
saveamberparams command, followed by a saveamberparm to generate the prmtop and
prmcrd files.
Please let me know if I am doing it correctly this time. I am attaching the p2n,
the mol2, the OFF and frcmod files that I am using for the calculation.
Thanks once again for all your help and I would look forward to your reply.
Best Regards,
Moitrayee
> 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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- application/octet-stream attachment: CIT.mol2
- application/octet-stream attachment: CIT.off
Received on Mon Jan 21 2013 - 10:00:02 PST
