[CP2K:3533] restraint dihedral

Campomanes Ramos Pablo pablo.ca... at epfl.ch
Mon Oct 17 17:21:00 CEST 2011


Dear Jacopo,

the problem comes from the fact that you are trying to read molecule names from AMBER topology files. This kind of files only store information about residue names, and therefore CP2K assigns new (different) MOLNAMEs.

Have a look at the previous discussion about this issue in the mailing list (Title: "Constraint warning with AMBER PDB file") where you can find a way to circumvent the problem based on the dumping of new PSF and PDB files which you can modify to give the MOLNAME information expected by cp2k.

Cheers,
Pablo.


________________________________
From: cp... at googlegroups.com [cp... at googlegroups.com] on behalf of Jacopo Sgrignani [sgr... at gmail.com]
Sent: Monday, October 17, 2011 3:46 PM
To: cp... at googlegroups.com
Subject: Re: [CP2K:3533] restraint dihedral

Dear Pablo
The input files are in the tar archive.
Actually, I found a post in this list about a similar problem with AMBER prmtop files.
Then I tried to put the number (456) of the molecule analysing the output of the MOLECULE print_key (it is the .mol file in the tar archive).
However the message is that the constrainted atoms are not in the 456 molecule.
Maybe I'm reading the molecule number in a wrong place.


Thanks again

Jacopo
2011/10/17 Campomanes Ramos Pablo <pablo.ca... at epfl.ch<mailto:pablo.ca... at epfl.ch>>
Dear Jacopo,

I think that the message is clear. The code cannot find the MOLNAME defined for constraints, and therefore I assume that constraints are not applied. However, it is difficult to guess where your problem is (pdb, topology file...) without having a look at your input(s) file(s)... Could you please post them here?

Regards,
Pablo.

________________________________
From: cp... at googlegroups.com<mailto:cp... at googlegroups.com> [cp... at googlegroups.com<mailto:cp... at googlegroups.com>] on behalf of Jacopo Sgrignani [sgr... at gmail.com<mailto:sgr... at gmail.com>]
Sent: Monday, October 17, 2011 1:44 PM
To: cp... at googlegroups.com<mailto:cp... at googlegroups.com>
Subject: Re: [CP2K:3530] restraint dihedral

Thanks Pablo for your suggestion, I'm trying this solution.
However I have a problem with the keyword MOLNAME or MOLECULE<http://cp2k.berlios.de/manual/CP2K_INPUT/MOTION/CONSTRAINT/COLLECTIVE.html#list_MOLECULE>, actually
I tried both the keyword MOLECULE with the resid number from the PDB input file, and
the keyword MOLNAME with the resname fromthe pdb, but they don't seem to be the right solutions.
Actually using MOLECULE with the resname the simulation start but in the output I find this warning:


 *** 13:22:30 WARNING in topology_constraint_util:print_warning_molname     ***
 *** MOLNAME (ASD) was defined for constraints, but this molecule      ***
 *** name is not defined. Please check carefully your PDB, PSF (has         ***
 *** priority over PDB) or input driven CP2K coordinates. In case you may   ***
 *** not find the reason for this warning it may be a good idea to print    ***
 *** all molecule information (including kind name) activating the          ***
 *** print_key MOLECULES specific of the SUBSYS%PRINT section.
Then I used also the MOLECULES print_key but the number of the molecule where the constrainted atoms are, it is
the same of the resid number in the PDB.

Can somebody help me? Is it this waring important or the costraint is applied?

Thanks again

Jacopo

2011/10/16 Campomanes Ramos Pablo <pablo.ca... at epfl.ch<mailto:pablo.ca... at epfl.ch>>
Dear Jacopo,

I think you can easily solve your problem if you have a look at:

http://cp2k.berlios.de/manual/CP2K_INPUT/MOTION/CONSTRAINT/COLLECTIVE/RESTRAINT.html

Best regards,
Pablo.

-----------------------------------------------
Pablo Campomanes

Tel:++41-(0)21-693-0326<tel:%2B%2B41-%280%2921-693-0326>
Fax: ++41-(0)21-693-0320<tel:%2B%2B41-%280%2921-693-0320>
Email: pablo.ca... at epfl.ch<mailto:pablo.ca... at epfl.ch>


Laboratory of Computational
Chemistry and Biochemistry
BCH 4118 EPF Lausanne
CH-1015 Lausanne

------------------------------------------------

________________________________
From: cp... at googlegroups.com<mailto:cp... at googlegroups.com> [cp... at googlegroups.com<mailto:cp... at googlegroups.com>] on behalf of Jacopo Sgrignani [sgr... at gmail.com<mailto:sgr... at gmail.com>]
Sent: Sunday, October 16, 2011 4:09 PM
To: cp... at googlegroups.com<mailto:cp... at googlegroups.com>
Subject: [CP2K:3528] restraint dihedral

Dear All
I would like to know the best way to restrict a dihedral angle during a simulation.
Without any experience about this, I tried to use a fictitious Colvar putting two walls to define the space that the dihedral can freely explore.  Then, the program asks for a value of the SCALE variable during the metadynamics calculation, and I set this to 0.

However, I'm not sure that this is the correct solution to my problem.

Can somebody suggest me other solutions?

Thanks

Jacopo




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