Hi, Justin,
thank you for your reply.
I have just checked my .itp files.
I have 7 itp files:
- one is generated by doing genpr to define the restraints on the protein;
- six (two for each chain of my complex) are generated directly by pdb2gmx
(first step of my simulation).
The first itp file is ok: numbers are consecutive and starting from1.
The other six files have not consecutive numbers (I paste here the first
lines of one of these files):
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
4 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
Since they are automatically generated by pdb2gmx, how can I fix the
problem?
Thank you very much.
Annalisa
-----------------------------------------------------
Annalisa Bordogna
PhD. Student
DISAT - Università degli Studi di Milano Bicocca
Milano - Italy
-----------------------------------------------------
2009/4/6 Justin A. Lemkul <[email protected]>
>
>
> annalisa bordogna wrote:
>
>> Hi everybody,
>> I am setting up an MD run on a peptide-protein complex with gromacs. I
>> have defined the box and solvated the system, but now I'd like to
>> equilibrate the solvent, so I tried with grompp, but an error occurs:
>>
>> Fatal error:
>> Residue numbers in the .top are not numbered consecutively from 1
>>
>> I paste here my file .top:
>>
>> ; Include forcefield parameters
>> #include "ffG43a2.itp"
>>
>> ; Include chain topologies
>> #include "a.complex_A.itp"
>> #include "a.complex_B.itp"
>> #include "a.complex_C.itp"
>>
>> ; Include water topology
>> #include "spc.itp"
>>
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ; i funct fcx fcy fcz
>> 1 1 1000 1000 1000
>> #endif
>>
>> ; Include generic topology for ions
>> #include "ions.itp"
>>
>> [ system ]
>> ; Name
>> Protein in water
>>
>> [ molecules ]
>> ; Compound #mols
>> Protein_A 1
>> Protein_B 1
>> Protein_C 1
>> SOL 28799
>>
>> I have searched in the wiki and in the archives of the mailing list, but I
>> have found no hints on how I could fix it.
>> Does anybody know how can I manage to make grompp work?
>>
>>
> The problem actually pertains to (at least) one of the chains you've
> included. Numbering is inconsistent in that file. Check the .itp files and
> make sure the atoms are numbered consecutively.
>
> -Justin
>
> Thank you in advance,
>> best regards,
>> Annalisa
>>
>> -----------------------------------------------------
>> Annalisa Bordogna
>> PhD. Student
>> DISAT - Università degli Studi di Milano Bicocca
>> Milano - Italy
>> -----------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list [email protected]
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to [email protected].
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list [email protected]
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to [email protected].
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
