[gmx-users] all-angle constraints

[Justin Lemkul]

On 7/21/12 2:13 AM, Mark Abraham wrote:
> On 21/07/2012 3:44 PM, radhika jaswal wrote:
>
> When replying to a digest, do change the subject to something useful, and do not
> include the entire digest in your email. People have better things to do than
> scroll through lots of text to find the relevant part.
>
>> Dear Sir,
>> I am using the ffG43a1 force field. Mine is an unusual unusual peptide and got
>> the necessary files from prodrg server.
>
> So perhaps you should examine its output and see whether hybridization makes
> sense then, before you worry about doing anything else. Garbage from a broken
> earlier step causes garbage later. If you aren't using prodrg properly,
> everything else is irrelevant.
>
>> and also pasting the top file. Please tell where , m making the mistake.
>
> Unfortunately that's impossible, because you are #including topology files that
> you are not showing us, nor have you described your molecule to us. Likely
> nmab2.itp is not well formed.
>

Indeed, PRODRG produces very unreliable output and you should not use its 
topologies without considerable modifications.  Amino acid residues will have 
parameters that are completely wrong.

http://pubs.acs.org/doi/abs/10.1021/ci100335w

-Justin

>>
>>
>>   The Force Fields to be included
>> #include "ffG43a1.itp"
>>
>> ; Include nmab2 topology
>> #include "nmab2.itp"
>>
>> ; Include water topology
>> #include "spc.itp"
>>
>> ; Include position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>>
>>
>> #ifdef POSRE_WATER
>> ; Position Restraint for each water oxygen
>> [ position_restraints ]
>> ; i funct        fcx          fcy        fcz
>>    1   1         1000         1000       1000
>> #endif
>
> These position restraints sections are not correctly located, but this is not
> your problem right now. See
> http://www.gromacs.org/Documentation/How-tos/Position_Restraints
>
> Mark
>
>>
>> [ system ]
>> ; Name
>> DRG in water
>>
>> [ molecules ]
>> ; Compound        #mols
>> DRG                 1
>>
>> SOL               397
>>
>> Thanks Sir.
>> Radhika
>>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================