Supported file types

[Devon Dillon]

I have read in the manual that votca supports .gro and .pdb files and as of now my goal is to map the trajectories, calculate charge transport integrals, an then charge mobility. I already have the crystal structures in .pdb and .gro format. I'm in the need of some feedback because the manual is not specific about where the .xml format comes from. My skills consist of being able to navigate the terminal, so I'm pretty basic. What do I need to do to calculate the charge transfer integrals and map the trajectories. I'm able to do reorganization energies in another program. Looking forward to learning and interacting with everyone!

[Jens Wehner]

the xml file you have to write yourself. THe tool pdb2map can help you, but in the end using a texteditor and a visualisation program e.g. vmd/pymol/jmol is helpful.

[Devon Dillon]

is there an example of how my xml file needs to be written? How does a visualization program help?

[Jens Wehner]

In the manual you find an example. Visualisation prgramm helps because you have to identify the MD-Atom with a QM-Atom so you need the numbering. Making the xml file, which we normally call the mapping file, is more art then anything else.

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[Devon Dillon]

Im having trouble using the pdb2map tool just to get a head start on the .xml file. Is there anyway you could give me some pointers? I really need an example command line of how to use the pdb2map and pdb2top tools. Please... What are the MD and QM-Atoms? How can i get the numbering? thank you in advance. 

[Jens Wehner]

Heyho,

Yeah the documentation is rather sparse. In the Manual under input you find an example mapping file. The command for pdb2map is ctp_tools -e pdb2map -o options.xml where options is not the mapping file but a file with the Options. You find out about the options by typing ctp_tools -d pdb2map.

The mapping is between the Atoms in your MD calculation and the Atoms in the corresponding dft calculation. Read the Manual first. Maybe tomorrow I can follow up with more.

Under votca/share you also find example XML Files

Am 22.09.2016 7:38 nachm. schrieb "Devon Dillon" <devondi...@gmail.com>:

Im having trouble using the pdb2map tool just to get a head start on the .xml file. Is there anyway you could give me some pointers? I really need an example command line of how to use the pdb2map and pdb2top tools. Please... What are the MD and QM-Atoms? How can i get the numbering? thank you in advance. 

[Devon]

Yes, I will look into making a file with options and keep you posted. Thank you for all your help. 😜

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[Devon Dillon]

so i made an options.xml file but the format is a bit unclear in the manual. i put everything in like this 

<pdb2map>

                <pdb> name of pub file<pdb>

<pdb2map>

-----------

i then typed in the command 

ctp_tools -e pdb2map -o options.xml

-----------

i get an error saying no MD (PDB,GRO) file provided. ???

i even tried putting the whole pdb file into the options.xml file between <pdb> <pdb> and got the same error. what am i doing wrong?

[Jens Wehner]

Okay,

a file should look like this

<options>

<pdb2map help="Converts MD + QM files to VOTCA mapping. Combinations: pdb+xyz,gro+xyz,pdb" label="calc:pdb2map" section="sec:pdb2map">
        <pdb help="Input pdb file" default="conf.pdb">conf_single.pdb</pdb>
        <gro help="Input gro file" default="conf.gro"></gro>
        <xyz help="Input xyz file" default="conf.xyz">8-PNP-O12.xyz</xyz>
        <xml help="Resulting xml file" default="conf.xml">system.xml</xml>
</pdb2map>

</options>

So you have your .pdb or .gro file of a single molecule

and the corresponding xyz file

.pdb or .gro files are from MD and xyz from QM

Cheers Jens

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[Devon]

So I have the .pdb and .xyz for a full crystal. Will this work the same way?

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[Jens Wehner]

try it my guess no

[Devon Dillon]

Is there anyway for me to create a co-crystal using the pdb2map tool with two pdb and xyz files?

[Jens Wehner]

Devon, I am not really sure what you want to do..........

So what do you specially want to do?

I suggest reading the manual first, then do the tutorial and then come back.

2016-09-26 20:25 GMT+02:00 Devon Dillon <devondi...@gmail.com>:

Is there anyway for me to create a co-crystal using the pdb2map tool with two pdb and xyz files?

[Devon Dillon]

Now i need to generate a topology and trajectory file so i can map the trajectory. Then i want to use the state file to generate a neighborlist and from there calculate the transfer integrals using DFT and the DIPRO method, and finally I want to calculate transfer rates. 

On Monday, September 26, 2016 at 6:11:20 PM UTC-5, Jens Wehner wrote:

Devon, I am not really sure what you want to do..........

So what do you specially want to do?

I suggest reading the manual first, then do the tutorial and then come back.

2016-09-26 20:25 GMT+02:00 Devon Dillon <devondi...@gmail.com>:

Is there anyway for me to create a co-crystal using the pdb2map tool with two pdb and xyz files?

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[Jens Wehner]

Okay, that is outlined in the manual. To create the topology and trajectory file you should have to use another grogramm

if you want to have a crystal with thermal fluctutations use gromacs e.g. Molecular Dynamics

if you want a pefect crystal you can build it by hand from your QM-calculations.

But that is all stuff you have to do before you use VOTCA

Cheers Jens

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[Devon Dillon]

i don't see how I'm supposed to get the topology.tpr or traj.xtc files i used the pdb2top tool in votca-ctp but that produces a .top file. What program do i need to use to produce a trajectory.xtc and topology.tpr. i already have the perfect crystal built. 

[Jens Wehner]

Why do you want to do it on a perfect crystal?

If you want to it a unit cell of your crystal is enough. You have the top file and the .pdb/.gro file easiest is probably to generate from a gromacs run.

Cheers Jens

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