OK I’ll try that thanks!
Fabian
____________________
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
fglaser.technion.ac.il
Tel: +972 4 8293701
http://bku.technion.ac.il
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
> On Sep 16, 2015, at 6:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> You can do it indirectly via the 'molinfo' command and some scripting.
> What I would do is first call cpptraj with 'molinfo' on whatever range
> I know I will need:
>
> cpptraj topology.parm7 > molinfo.tmp <<EOF
> molinfo :1-264
> EOF
>
> The output of molinfo looks like so:
> #Mol Natom #Res Name
> 1 220 1 SER
> 2 3 14 WAT SOLVENT
> 3 3 15 WAT SOLVENT
> ...
>
> Then you just parse the third column to generate masks for whatever
> action using your favorite scripting language (I'll post an example
> below). However, I really need to get the mask parser to understand
> molecules. I'll make that a priority.
>
> Hope this helps,
>
> -Dan
>
> Example to generate input (should work but not extensively tested:
>
> #!/bin/bash
>
> # Topology
> TOP=tz2.truncoct.parm7
> # Last residue in selection
> LASTRES=20
> # Command
> CMD=surf
>
> cpptraj $TOP > tmp <<EOF
> molinfo :1-$LASTRES
> EOF
>
> awk -v cmd=$CMD -v lastres=$LASTRES 'BEGIN{
> readInfo = 0;
> res0 = -1;
> ncmd = 1;
> }{
> if (readInfo == 1 ) {
> if (NF != 4 && NF != 5) exit 0;
> if (res0 != -1)
> printf("%s :%i-%i out surf%i.out\n", cmd, res0, $3 - 1, ncmd++);
> res0 = $3;
> } else if ( $1 == "#Mol" )
> readInfo = 1;
> }END{
> printf("%s :%i-%i out surf%i.out\n", cmd, res0, lastres, ncmd);
> }' tmp
>
> rm tmp
>
>
> On Thu, Sep 10, 2015 at 4:05 AM, Fabian gmail <fabian.glaser.gmail.com> wrote:
>> Hi,
>>
>> I have a situation in which my input file contains 12 peptides, which in the PDB are separated by a TER. Now I would like to calculate all kind of parameters like “lie” or “surf” on each of those fragments on the cpptraj analysis file. But without doing it manually.
>>
>> Is there a way to identify from the .prmtop or the .inpcrd the different molecules I have and thus to identify the numlist mask numbers of each peptides such that I could automatically write syntax like:
>>
>> #energies of interaction
>> surf :1-22 out surf1.out
>> surf :23-44 out surf2.out
>> surf :45-66 out surf3.out
>> surf :67-88 out surf4.out
>> surf :89-110 out surf5.out
>> surf :111-132 out surf6.out
>> surf :133-154 out surf7.out
>> surf :155-176 out surf8.out
>> surf :177-198 out surf9.out
>> surf :199-220 out surf10.out
>> surf :221-242 out surf11.out
>> surf :243-264 out surf12.out
>>
>> But again, doing it such that the mask numbers of each pepptide will be idenfied automatically?
>>
>> At the moment I do it manually for each variant… a lot of manual work.
>>
>> Best regards,
>>
>> fabian
>>
>> ____________________
>> Dr. Fabian Glaser
>> Head of the Structural Bioinformatics section
>> Bioinformatics Knowledge Unit - BKU
>>
>> fglaser.technion.ac.il
>> Tel: +972 4 8293701
>>
>> http://bku.technion.ac.il
>> The Lorry I. Lokey Interdisciplinary
>> Center for Life Sciences and Engineering
>> Technion - Israel Institute of Technology
>> Haifa 32000, ISRAEL
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Sep 16 2015 - 08:30:12 PDT
