[gmx-users] long-stick molecule solvation

[xy21hb]

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
 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


Many thanks,

Yao








At 2015-11-04 20:55:31, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 11/4/15 7:53 AM, xy21hb wrote:
>> Hi Justin,
>>
>> thanks for your reply. I actually just followed your tutorial on lysozyme.
>> I did not set any termini or merge any chains.
>>
>
>Without the exact information I requested, there's nothing anyone can do to help 
>you.  Please provide it.  Descriptions of what you did (or what you think you 
>did) mean far less than actual input and output from the terminal, especially 
>pdb2gmx.  The DD information about bonds suggests something is wrong with the 
>topology.  Since pdb2gmx generates the topology, this is where we need to start.
>
>-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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