Thank you so much. are 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 there?
On Tue, Jan 30, 2018 at 5:49 PM, roja rahmani <roja.rhmn.gmail.com> wrote:
> 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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>>
>
>
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Received on Tue Jan 30 2018 - 06:30:04 PST
