On Tue, Jan 30, 2018 at 7:08 PM, ABEL Stephane <Stephane.ABEL.cea.fr> wrote:
> GROMACS contains Thr with NH3+ and COO- termini so you can a thr residue
> without problem. Please note that it is "not" a Amber issue so it is the
> wrong forum to ask your question.
>
> S
>
> ----------------------------------------------------------
> Stéphane Abel, Ph.D.
> Commissariat à l’Energie Atomique et aux Energies Alternatives
> Centre de Saclay DSV/ISVFJ/SB2SM
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> ________________________________________
> De : roja rahmani [roja.rhmn.gmail.com]
> Envoyé : mardi 30 janvier 2018 15:50
> À : AMBER Mailing List
> Objet : Re: [AMBER] Empty .frcmod file
>
> I want AA(THR) as a an separate structure not as protein residue.
> when i use pdb2gmx for threonine.pdb, i afce with an error; THR is not
> identified ...
>
> On Tue, Jan 30, 2018 at 6:04 PM, ABEL Stephane <Stephane.ABEL.cea.fr>
> wrote:
>
> > BTW,
> >
> > the gromacs distribution already contains Amber parameters you need for
> > threonine
> >
> > Stephane
> > ----------------------------------------------------------
> > Stéphane Abel, Ph.D.
> > Commissariat à l’Energie Atomique et aux Energies Alternatives
> > Centre de Saclay DSV/ISVFJ/SB2SM
> > Bat 528, Office 138C
> > Gif-sur-Yvette, F-91191 FRANCE
> > Phone (portable) : +33 6 49 37 70 60
> > ________________________________________
> > De : roja rahmani [roja.rhmn.gmail.com]
> > Envoyé : mardi 30 janvier 2018 15:19
> > À : AMBER Mailing List
> > Objet : Re: [AMBER] Empty .frcmod file
> >
> > Thank you so much. is these parameters usable for amber99 too?or i should
> > modify its atom types?
> > and how can i use this .prmtop file as an input for GROMACS? is it
> > identified?
> >
> > On Tue, Jan 30, 2018 at 5:21 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> > wrote:
> >
> > > Hi,
> > > I see nothing wrong in this.
> > > Empty frcmod file only means gaff has all the parameters for this.
> > >
> > >
> > > Best Regards
> > > Elvis Martis
> > > Mumbai, INDIA.
> > >
> > > ________________________________________
> > > From: roja rahmani <roja.rhmn.gmail.com>
> > > Sent: 30 January 2018 19:09
> > > To: amber.ambermd.org
> > > Subject: [AMBER] Empty .frcmod file
> > >
> > > Hello,
> > >
> > > This is threonine.pdb;
> > >
> > > ATOM 1 N THR 1 0.080 -0.083 0.000 1.00 0.00
> > > ATOM 2 CA THR 1 1.539 -0.033 0.000 1.00 0.00
> > > ATOM 3 C THR 1 2.032 1.394 0.000 1.00 0.00
> > > ATOM 4 O THR 1 1.268 2.339 0.000 1.00 0.00
> > > ATOM 5 CB THR 1 2.116 -0.818 -1.226 1.00 0.00
> > > ATOM 6 OG1 THR 1 1.743 -2.188 -1.162 1.00 0.00
> > > ATOM 7 CG2 THR 1 3.654 -0.842 -1.361 1.00 0.00
> > > ATOM 8 1H THR 1 -0.523 0.813 0.000 1.00 0.00
> > > ATOM 9 2H THR 1 -0.461 -1.018 0.000 1.00 0.00
> > > ATOM 10 HA THR 1 1.904 -0.508 0.929 1.00 0.00
> > > ATOM 11 HB THR 1 1.691 -0.378 -2.154 1.00 0.00
> > > ATOM 12 HG1 THR 1 2.066 -2.592 -1.973 1.00 0.00
> > > ATOM 13 1HG2 THR 1 3.986 -1.433 -2.235 1.00 0.00
> > > ATOM 14 2HG2 THR 1 4.083 0.168 -1.502 1.00 0.00
> > > ATOM 15 3HG2 THR 1 4.138 -1.279 -0.467 1.00 0.00
> > > ATOM 16 OC THR 1 3.452 1.567 0.000 1.00 0.00
> > > ATOM 17 HC THR 1 3.911 0.645 0.000 1.00 0.00
> > > TER
> > > ~
> > >
> > >
> > > I usedthis command;
> > > antechamber -i threonine.pdb -fi pdb -o threonine.mol2 -fo mol2 -c bcc
> > -s 2
> > >
> > > Welcome to antechamber 17.3: molecular input file processor.
> > >
> > > acdoctor mode is on: check and diagnosis problems in the input file.
> > > -- Check Format for pdb File --
> > > Status: pass
> > > -- Check Unusual Elements --
> > > Status: pass
> > > -- Check Open Valences --
> > > Status: pass
> > > -- Check Geometry --
> > > for those bonded
> > > for those not bonded
> > > Status: pass
> > > -- Check Weird Bonds --
> > > Status: pass
> > > -- Check Number of Units --
> > > Status: pass
> > > acdoctor mode has completed checking the input file.
> > >
> > > Running: /home/roja/amber17_FIRST/bin/bondtype -j full -i
> > > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> > >
> > > Running: /home/roja/amber17_FIRST/bin/atomtype -i ANTECHAMBER_AC.AC0
> -o
> > > ANTECHAMBER_AC.AC -p gaff
> > > Info: Total number of electrons: 64; net charge: 0
> > >
> > > Running: /home/roja/amber17_FIRST/bin/sqm -O -i sqm.in -o sqm.out
> > >
> > > Running: /home/roja/amber17_FIRST/bin/am1bcc -i
> > ANTECHAMBER_AM1BCC_PRE.AC
> > > -o ANTECHAMBER_AM1BCC.AC -f ac -p
> > > /home/roja/amber17_FIRST/dat/antechamber/BCCPARM.DAT -s 2 -j 1
> > >
> > > Running: /home/roja/amber17_FIRST/bin/atomtype -f ac -p bcc -o
> > > ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
> > >
> > > these are my files;
> > >
> > > ANTECHAMBER_AC.AC ANTECHAMBER_AM1BCC_PRE.AC ATOMTYPE.INF sqm.out
> > > threonine.mol2
> > > ANTECHAMBER_AC.AC0 ANTECHAMBER_BOND_TYPE.AC sqm.pdb threonine.pdb
> > > ANTECHAMBER_AM1BCC.AC ANTECHAMBER_BOND_TYPE.AC sqm.in
> > >
> > >
> > > then i use this command;
> > > parmchk -i threonine.mol2 -f mol2 -o threonine.frcmod
> > >
> > > but the threonine.frcmod file is empty;
> > >
> > > remark goes here
> > > MASS
> > >
> > > BOND
> > >
> > > ANGLE
> > >
> > > DIHE
> > >
> > > IMPROPER
> > >
> > > NONBON
> > >
> > > ~
> > > ~
> > >
> > > Could you please help me how can i fix it?
> > >
> > > With regards
> > > Nick
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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Received on Tue Jan 30 2018 - 08:30:03 PST
