[gmx-users] long-stick molecule solvation

[xy21hb]

Dear Justin,

Many thanks for pointing out the error. You are right. After fixing the MET, everything works fine.

Best,

Yao









At 2015-11-04 22:31:25, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 11/4/15 9:22 AM, xy21hb wrote:
>>
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>> Dear Justin,
>>
>> Below are the commands I used with all the files attached.
>>   https://drive.google.com/file/d/0B4Quti6TfNU_djIwYUZvX3U5NHc/view?usp=sharing
>>
>>
>>   pdb2gmx -f 4KE2.pdb -missing -ignh -o double
>
>Never use -missing.
>
>>   gmx editconf -f double.gro -o d-box -c -d 0.5 -bt triclinic -princ
>>   gmx solvate -cp d-box.gro -cs spc216.gro -o d-solv.gro -p topol.top
>>   grompp -f em.mdp -c d-solv.gro -p topol.top -o em
>>   mdrun -v -s em
>>
>
>If you visualize d-solv.gro you will see that you have ridiculous coordinates 
>for HB atoms in the 0MET residue; this is the cause of your problem, and mdrun 
>points you to this fact directly:
>
>WARNING: Listed nonbonded interaction between particles 1 and 8
>at distance 6.219 which is larger than the table limit 2.000 nm.
>
>Atom 1 is the N-terminal N, and atom 8 is HB1.
>
>Note also that you have made your box fit very tightly to your protein, and any 
>small amount of rotation will lead to unphysical interactions and minimum image 
>violations.
>
>-Justin
>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
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