Thanks Jason and François,
It works very fine with the RED server following the procedure below. I
had some missing force field parameters but I found them in the literature.
If the missing parameters are not available, which solution is the more
straighforward to obtain them and fill the user.frcmod?
Best wishes,
Baptiste
Le 16/07/2014 08:20, FyD a écrit :
> Dear Baptiste,
>
> The total charge of a molecular fragment originating from a molecule
> has to be an integer, and this can be only achieved by applying
> specific charge constraint(s) during the charge fitting step.
>
> You could use R.E.D. Server Dev./PyRED at
> http://q4md-forcefieldtools.org/REDServer-Development/
> See
> http://q4md-forcefieldtools.org/REDServer-Development/news.php
> http://q4md-forcefieldtools.org/REDServer-Development/Documentation/
>
> See the corresponding tutorial:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
>
> PyRED generates an empirical force field (force field libraries +
> force field parameters) and a LEaP script for input molecules and
> molecular fragments.
>
> In your case read:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#16
> vs
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#25
> vs
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#26
>
> once the job is done you end up with a leap script:
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#6
>
> tar -jxvf P$x.tar.bz2
> cd P$x/Data-R.E.D.Server/Data-Default-Proj
> xleap -f leaprc.q4mdfft
>
> That means no need to load gaff + amber99 + whatever additional force
> field_s_ and no need to load tons of useless atom types ;-)
> A single force field is generated based on parm99, and a user can even
> provide missing and/or mandatory force field parameters as input via
> the frcmod.user file (see
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#9).
> Thus only required force field atom types/parameters are generated
> (generic dihedral force field parameters are also converted into
> specific ones to prepare MM vs QM dihedral fit etc...).
>
> I hope this helps...
>
> regards, Francois
>
>
>> I tried diverses strategies to get resp charges of an exotic amino acid
>> (a dipeptide actually) and to incorporate it in a peptide sequence but
>> without success (not an integer) . Can you give me your opinion, please?
>> For example:
>>
>> First, I built a pdb of my modified residue (NH2-MOD-COOH) then I
>> launched antechamber:
>> antechamber -i MOD.pdb -fi pdb -o ./MOD.prepin -fo prepi -c bcc -s 2 >
>> antechamber.out
>> parmchk -i MOD.prepin -f prepi -o MOD.frcmod (and I completed the frcmod
>> file manually to fit parm99.dat)
>>
>> In parallel, I built the ACE-MOD-NME fragment (MOD-cap.pdb) to derive
>> the charge using the RED server and to modify the charges directly in
>> the prepin.
>>
>> Then, I used leap:
>>
>> source leaprc.gaff
>> source leaprc.ff99SB
>> loadamberprep MOD.prepin
>> loadamberparams MOD.frcmod
>> remove MOD MOD.1.H29 (remove a H from the NH2)
>> remove MOD MOD.1.H30 (remove the H from the COOH)
>> set MOD head MOD.1.N1
>> set MOD tail MOD.1.C5
>> tri = sequence { NALA MOD CALA}
>> saveamberparm tri tri.prmtop tri.inpcrd
>>
>> Finally, except the charges, the generated files seems to be correct. I
>> also tried to calculate the charges only using antechamber and/or via a
>> mol2 file generating a new library.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 17 2014 - 01:00:02 PDT
