Hi Francois,
I am trying to generate the parameters for a modified amino acid on the red
server. My job id is P3051. I am using the fragment based approach. I started
with ACE-XXX-NME, generated the p2n file, checked for chemical equivalencing and
submitted it the red server for mol2 file generation. I also read through
tutorial
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
However, I am am getting very confused with the different .mol2 files being
generated. It would be really helpful if you please suggest how should I proceed
with this.
Thanks a lot.
Best Regards,
Moitrayee
> Dear Moitrayee,
>
> This looks like far better. Last comments:
>
> - So far the mol3 file format is mainly useful for molecular
> fragments. You have a whole molecule; thus, the mol2 file format is
> the best choice (i.e. it can be used as a FF lib in the LEaP program
> and easily displayed in a graphical program such as vmd where
> topology, atom names, charges values (& atom types) can be visually
> checked; and it is directly generated by R.E.D.)...
>
> - If you use leaprc.ff99SB (or any newer version) I do not think so
> you need to build a new frcmod file. All the FF parameters for citrate
> should be in parm99.dat. Moreover, my feeling is that such an accuracy
> for bond & angle FF constants in gaff.dat is useless; just compare the
> values in gaff.dat vs parm99.dat, and read the original papers
> (parm96, parm98 & parm99).
>
> For instance:
> [fyd.master0 parm]$ egrep "^c3-c3 " gaff.dat
> c3-c3 303.1 1.5350 SOURCE1 14664 0.0048
> [fyd.master0 parm]$ egrep "^CT-CT " parm99.dat
> CT-CT 310.0 1.526 JCC,7,(1986),230; AA, SUGARS
> -> such an accuracy "303.1" is meaningless: better using parm99.dat...
> Same remark for:
> [fyd.master0 parm]$ egrep "^c3-h1 " gaff.dat
> c3-h1 335.9 1.0930 SOURCE3 2175 0.0082
> [fyd.master0 parm]$ egrep "^CT-H1 " parm99.dat
> CT-H1 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, RIBOSE
> -> such an accuracy "335.9" is meaningless: better using parm99.dat...
>
> - The off file format has the same role than the mol3/mol2 file format(s).
>
> - I would first try to only constraint the HO-OH-CT-H1 dihedral (in
> the QM geometry optimization).
>
> - At the end, I would only execute:
> xleap -f leaprc.ff99SB
> VAR = loadmol2 CIT.mol2
> saveamberparm VAR VAR.top VAR.crd
>
> regards, 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.
>
>>> 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 Thu Feb 28 2013 - 10:00:03 PST
