ram bio wrote:
Dear Gromacs Users,
Thanks Justin and Marc for the response and you were right.
As suggested, i had a view in the modelled protein pdb file and here
both the terimus are capped that is as follows;
ATOM 1 N THR A 62 -43.095 3.360 19.026 1.00 30.00 N1+
ATOM 4804 OXT PRO A 355 -53.907 34.064 13.899 1.00110.00 O1-
then i tried to execute the pdb2gmx command as under, (which i did
earlier also): pdb2gmx -f damgomu.pdb -o damgomu_processed.gro -ignh
-ter -water spc
and selected the "Gromos96 53a6" parameter and "none" options, then
the warnings and errors where as follows:
Why would you choose "None?" It would seem that you do not, in fact, have
capping groups. If atom 1 is the N of THR, then there is no ACE cap before it...
Now there are 294 residues with 3043 atoms
Making bonds...
Warning: Long Bond (12-14 = 0.65447 nm)
Warning: Long Bond (1975-1977 = 4.21722 nm)
Warning: Long Bond (2050-2052 = 3.24295 nm)
These messages generally indicate missing atoms. Investigate what they are and
why these errors are coming up.
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: atom H is missing in residue THR 1 in the pdb file
You might need to add atom H to the hydrogen database of residue THR
in the file ff???.hdb (see the manual)
This warning comes from the fact that you are telling pdb2gmx to look for
capping groups in order to find improper dihedrals, and it appears no such
groups exist.
Fatal error:
There were 1 missing atoms in molecule Protein_A, if you want to use
this incomplete topology anyhow, use the option -missing
and in the previous run i concatenated -missing option and continued
further, then the toplogy was written with the charge of Total charge
12.690 e ,but still the warning persisted of missing H atom in THR1.
There is a reason the pdb2gmx help information calls the -missing option
"dangerous"...
Please suggest me how to rectify this error and why the total number
of atoms in pdb file (4815) are not matching even though the number of
residues are matching after pdb2gmx step.
Find out which atoms are missing (if any) to fix the "long bonds" problem, then
don't specify "None" as your termini unless you really have acetyl and amide caps.
-Justin
Thanks,
Ram
and selected choose the "Gromos96 53a6" parameter and "none" options
On Tue, Sep 29, 2009 at 7:04 PM, Justin A. Lemkul <[email protected]> wrote:
ram bio wrote:
Dear Gromacs users,
I have a modelled protein whose net charge is +12.69, and I would like to
ionize the protein to make it neutral using genion command, but in genion
command we can add a specific number of postive or negative charged ions which
for my case would not completely neutralize the system and i learnt from Justin
tutorial that we can even neutralize it using -conc and -neutral options in
conjugation. As I am running a membrane-protein simulation, I would like to
know the command which I am using is correct or not.
genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA+ -nname CL-
-nn 12 -neutral
If my command is wrong Please suggest the right one as In future i have to
conjugate SOL and CL- ions to create a special index file.
If your protein has a net charge of +12.69, it is probably wrong. Does
anything in real life have such a net fractional charge?
Go back and evaluate what you have done. Are there missing atoms? Wrong
parameters? The genion command you want to use is fine, but is not suitable
for your system in its current state.
-Justin
Thanks
Ram
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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send it to [email protected].
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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