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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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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Received on Wed Sep 16 2015 - 08:30:03 PDT
