[gmx-users] pdb2gmx disulfide bond in dimer

[s.varriale]

thank you Justin, but I can't understand how to solve my  problem.
when pdb2gmx links the 2 CYS, the resulting .gro file shows a unique 
chain because  N- and C- termini of 2 chains are linked.

Sonia
Il 14/04/2016 13:46 Justin Lemkul ha scritto:
> On 4/14/16 6:32 AM, s.varriale wrote:
>> 
>> Dear all,
>> I try to perform a MD simulation of a covalent dimer with gromacs 
>> 4.5.4.
>> I do:
>> pdb2gmx -f prot.pdb -chainsep ter
>> and the programme generates a .gro file with disulfide bond.
>> but when i want to minimize the system, there is an error:
>> 
>> There were 2 inconsistent shifts. Check your topology
>> Warning: 1-4 interaction between 45 and 387 at distance 8.995 which is 
>> larger
>> than the 1-4 table size 2.200 nm
>> 
>> if I try to simulate the 2 chains separatly, there is any error.
>> What can i do?
> 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> 
> -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
> 
> ==================================================

-- 
Sonia Varriale, PhD