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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>
--
“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 Sun Nov 15 2020 - 11:30:02 PST
