Dear Ankita,
Check again the numbering and pdb labels in your pdb files.
For inistance i see HG2 in RGP1 has been renamed HG1 in UNK2 and vice versa.
Best
George
> Thank You so much for your response!
> Here I have attached the topology and coordinate file I am using.
>
> On Mon, Nov 16, 2020 at 12:53 AM Giorgos Lambrinidis <
> lamprinidis.pharm.uoa.gr> wrote:
>
>> Dear Ankita,
>>
>> The error is related to the atom numbering of the two ligands. Can you
>> attach the topology and coordinate file you utilized for further
>> inspection?
>>
>> Dr. George Lamprinidis
>>
>> > Dear users,
>> >
>> > It's a gentle reminder.
>> > Any suggestions or comments would be very helpful.
>> > Thank you in advance!
>> >
>> > Kind regards
>> > Ankita Tripathi
>> >
>> > On Thu, Nov 12, 2020, 6:49 PM Ankita Tripathi <at194.snu.edu.in>
>> wrote:
>> >
>> >> Dear Users,
>> >> I am very new to thermodynamic integration. I have successfully done
>> the
>> >> TI tutorial for amber that is available at
>> >> http://ambermd.org/tutorials/advanced/tutorial9 without any problems
>> or
>> >> warnings.
>> >>
>> >> Now I started implementing it on my system which includes one protein
>> >> and
>> >> two ligands Glutamyl phosphate(RGP) and N-Acetyl glutamyl
>> >> phosphate(UNK),
>> >> basically, I wanted to calculate the relative free energy.
>> >>
>> >> I have done the first step in the setup that is Setting up the
>> >> vdW+bonded
>> >> transformation step without any issue after that in the second step
>> >> Running
>> >> MD to provide sane starting coordinates I am getting the following
>> error
>> >> in
>> >> the minimization step
>> >> default_name
>> >> Mask !:WAT & !.H=; matches 36 atoms
>> >> TI Mask 1 :RGP; matches 22 atoms
>> >> TI Mask 2 :UNK; matches 26 atoms
>> >> TI region 1: 3627 atoms
>> >> TI region 2: 3631 atoms
>> >> SC Mask 1 :RGP.H1,HN1,HN2; matches 3 atoms
>> >> SC Mask 2 :UNK.O5,C6,C7,H6,H7,H8,H9; matches 7 atoms
>> >> Error : Atom 16 does not have match in V1 !
>> >>
>> >> I followed all the key points that are all the common atoms of
>> ligands
>> >> in
>> >> input files have identical starting coordinates, appear in the same
>> >> order,
>> >> share the same atom names.
>> >> I am attaching all the required input files.
>> >>
>> >> Any advice, suggestions would be of great help to me!
>> >> Thank You in advance.
>> >>
>> >> Kind Regards
>> >> Ankita Tripathi
>> >>
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> --
>> “Good judgement is the result of experience and experience the result of
>> bad judgement.”
>>
>> ― Mark Twain
>>
>> ---------------------------------------------
>> Dr George Lambrinidis
>> Researcher & Laboratory Assistant Staff
>> School of Health Sciences
>> Faculty of Pharmacy
>> National & Kapodistrian University of Athens
>> Greece
>> tel: +30 2107274304
>> +30 2107274521
>> fax: +30 2107274747
>> e-mail: lambrinidis.pharm.uoa.gr
>> geolampr.gmail.com
>> ---------------------------------------------
>>
>>
>>
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>>
> _______________________________________________
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>
--
“Good judgement is the result of experience and experience the result of
bad judgement.”
― Mark Twain
---------------------------------------------
Dr George Lambrinidis
Researcher & Laboratory Assistant Staff
School of Health Sciences
Faculty of Pharmacy
National & Kapodistrian University of Athens
Greece
tel: +30 2107274304
+30 2107274521
fax: +30 2107274747
e-mail: lambrinidis.pharm.uoa.gr
geolampr.gmail.com
---------------------------------------------
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Received on Mon Nov 16 2020 - 00:30:03 PST
