On 4/07/2011 11:49 PM, Emine Deniz Tekin wrote:
Hi Mark,
Thank you for your reply.
Let me explain the problem a little more and answer your questions. I
would be happy if you could expound upon your reply.
Sorry, I can't.
* I won't try to make sense of five different font styles and a forest
of differential indentation.
* You didn't say whether you tested the single lipopeptide topology like
I suggested. Solve simple problems completely before tackling complex
problems.
* I pointed out that showing us only the coordinate file was not an
effective way of diagnosing a mismatch of topology database and
coordinate file naming, and you still haven't supplied any topology
information.
* The *geometry* of the lipopetides is often irrelevant for trying to
get pdb2gmx to construct a *topology*
Mark
Hi Gromacs users,
I created a lipopeptide (lauroic acid connected to an 8-residue
peptide which starts with Valine).
How is the link from acid to peptide created?
The link between acid and peptide is a “peptide bond”.
(I prepared the *rtp *entry for the lauroic acid make a peptide bond as if
lauroic acid was an amino acid (following your suggestion)).
If I try to use “pdb2gmx” for ONE LİPOPEPTİDE (9 residues), that is
pdb2gmx –f one_lipopeptide.pdb -ter
It seems to work. That is, topol.top is created. (And also this
topology works for MD.)
Does that topology work for MD? Why does pdb2gmx think there's 9
residues, and below there seem to be 63?
·But, if I try to use “pdb2gmx” for SEVEN LİPOPEPTİDE at desired
positions (63 residues), that is
pdb2gmx –f seven_lipopeptide.pdb -ter
It gives the fatal error: “Atom N not found in residue seq.nr
<http://seq.nr/>. 1 while adding improper”
While I was creating the lipopeptide, I introduced the lauroic
acid as a pseudo amino acid (following Mark’s suggestion). So, I
really do NOT have atom N in the first residue. I pasted a part
of my gro file below.
Some improper in your topology database entries wants a N atom
that doesn't exist. Unfortunately, we don't have anywhere near
enough information to guess why. pdb2gmx is trying to match your
.rtp and specbond entries to your .gro file, but only seeing the
latter can't help diagnose a mismatch. Some description of
"desired positions" is also important.
I wrote a code to put 7 identical lipopeptides at desired positions.
That is, 7 lipopeptides are placed on a plane with 15 degree angle
between the adjacent lipopeptides.
Also, giving full command lines are always preferred. You may not
think anything significant is there, and you might be right, but
if there *can* be something significant there, and we aren't given
the chance to know whether it is present, we might just not bother
to waste time guessing :)
I used gromos53a6 force field (extended to include lauroic acid
parameters) & spc type water
And also, I have a question: The first residue in my pdb file is
lauroic acid that is DPP, second residue is Valine and so on.. But
when I used the pdb2gmx with –ter it says: Start terminus VAL-2: None,
End terminus ASP-9: COO-) Would not DPP residue be the start terminus?
Best regards,
Mark
Deniz
GROMACS molecule input test
574
1DPPCA111.0275.2953.153
1DPPCB210.8945.2993.078
1DPPCG310.7775.2343.153
1DPPCD410.6455.2543.078
1DPPCE510.5215.2033.153
1DPPCZ610.3925.2513.086
1DPPCM710.2665.2073.161
1DPPCN810.1405.2723.103
1DPPCO910.0145.2213.172
1DPPCP109.8855.2793.112
1DPPCQ119.7615.2033.160
1DPPC1211.1015.4303.147
1DPPO1311.0325.5313.136
2VALN1411.2355.4503.160
2VALH1511.2495.5503.159
2VALCA1611.3685.3853.181
2VALCB1711.3905.2333.181
2VALCG11811.3325.1723.308
2VALCG21911.3385.1613.056
2VALC2011.4865.4493.103
2VALO2111.4985.4362.982
…………..
63ASPOD1570-0.30614.8743.343
63ASPOD2571-0.45115.0303.289
63ASPC572-0.05715.0233.106
63ASPO15730.01415.0033.207
63ASPO2574-0.02915.1043.017
16.2393716.2393716.23937
I am using Gromacs 53a6 force field and gromacs 4.5.3 version.
Any help will be appreciated.
Thanks in advance
Deniz
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