Hey Christoph,
Thanks for the help. I got to know about the csg_dump command as soon as I
sent you the email. For some reason, csg_dump is categorizing all the atoms
as the valine molecules as ALA as well, which is counterintuitive to me.
But I did change my valine.xml file to:-
<cg_molecule>
<name>VAL</name>
<ident>VAL</ident>
<topology>
<cg_beads>
<cg_bead>
<name>VAL</name>
<type>VAL</type>
<mapping>A</mapping>
<beads>
1:ALA:CA 1:ALA:C 1:ALA:N 1:ALA:H1 1:ALA:H2 1:ALA:CB 1:ALA:HA
1:ALA:CG1 1:ALA:HG11 1:ALA:HG12 1:ALA:HG13 1:ALA:CG2 1:ALA:HB 1:ALA:HG21
1:ALA:HG22 1:ALA:HG23 1:ALA:O 1:ALA:OXT 1:ALA:HXT
</beads>
</cg_bead>
</cg_beads>
</topology>
<maps>
<map>
<name>A</name>
<weights>12 12 14 1 1 12 1 12 1 1 1 12 1 1 1 1 16 16 1</weights>
</map>
</maps>
</cg_molecule>
Now, I get a different error,
I have 8000 beads in 500 molecules
I have 500 beads in 500 molecules for the coarsegraining
1.1853
-0.2654
0.0787 1.2896
-0.2967
-0.0276
an error occurred:
coarse-grained bead is bigger than half the box
(atoms CA (id 1), C (id 2) , molecule 1)
Can you please tell me what I can change?
On Wed, Jul 7, 2021 at 3:29 PM Christoph Junghans <[email protected]>
wrote:
>
>
> On Wed, Jul 7, 2021 at 13:23 Rishabh Guha <[email protected]> wrote:
>
>> Hello,
>>
>> I have an atomistic system consisting of 250 alanine and 250 valine
>> molecules. I am trying to use cg_map using the pdb file and the LAMMPS
>> output trajectory, but I am getting an error:-
>> cannot find: <1:VAL:CA> in VAL
>> an error occurred:
>> mapping error: molecule 1:VAL:CA does not exist
>>
> try to run “csg_dump --top topol.xml” and check how VOTCA labels things.
>
> Christoph
>
>
>> My topology file looks like:-
>> <topology base="temp.pdb">
>> <molecules>
>> <clear/>
>> <define name="ALA" first="1" nbeads="13" nmols="250"/>
>> <define name="VAL" first="3251" nbeads="19" nmols="250"/>
>> </molecules>
>> </topology>
>>
>> My individual alanine and valine xml files are:-
>> Alanine-
>> <cg_molecule>
>> <name>ALA</name>
>> <ident>ALA</ident>
>> <topology>
>> <cg_beads>
>> <cg_bead>
>> <name>ALA</name>
>> <type>ALA</type>
>> <mapping>A</mapping>
>> <beads>
>> 1:ALA:CA 1:ALA:C 1:ALA:N 1:ALA:H1 1:ALA:H2 1:ALA:CB 1:ALA:HA
>> 1:ALA:HB1 1:ALA:HB2 1:ALA:HB3 1:ALA:O 1:ALA:OXT 1:ALA:HXT
>> </beads>
>> </cg_bead>
>> </cg_beads>
>> </topology>
>> <maps>
>> <map>
>> <name>A</name>
>> <weights>12 12 14 1 1 12 1 1 1 1 16 16 1</weights>
>> </map>
>> </maps>
>> </cg_molecule>
>>
>> Valine
>> <cg_molecule>
>> <name>VAL</name>
>> <ident>VAL</ident>
>> <topology>
>> <cg_beads>
>> <cg_bead>
>> <name>VAL</name>
>> <type>VAL</type>
>> <mapping>A</mapping>
>> <beads>
>> 1:VAL:CA 1:VAL:C 1:VAL:N 1:VAL:H1 1:VAL:H2 1:VAL:CB 1:VAL:HA
>> 1:VAL:CG1 1:VAL:HG11 1:VAL:HG12 1:VAL:HG13 1:VAL:CG2 1:VAL:HB 1:VAL:HG21
>> 1:VAL:HG22 1:VAL:HG23 1:VAL:O 1:VAL:OXT 1:VAL:HXT
>> </beads>
>> </cg_bead>
>> </cg_beads>
>> </topology>
>> <maps>
>> <map>
>> <name>A</name>
>> <weights>12 12 14 1 1 12 1 12 1 1 1 12 1 1 1 1 16 16 1</weights>
>> </map>
>> </maps>
>> </cg_molecule>
>>
>> I have attached the pdb file for further reference.
>>
>> Can anyone please help me with this?
>>
>> --
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>> .
>>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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--
Rishabh Debraj Guha(PhD student)
Graduate Research Assistant
Mechanical and Aerospace Engineering
North Carolina State University
Contact:- +1-347-205-2280
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