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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Received on Tue Jan 30 2018 - 06:30:03 PST
