[gmx-users] neutralizing membrane protein in lipid bilayer +water
rmbio861 at gmail.com
Tue Sep 29 17:55:51 CEST 2009
When I observed the toplogy file the first THR moeity was missing in 1
hydrogen atom compared to other Thr in the file so i added one line
below the 1st atom nitrogen for hydrogen as under and corrected the
qtot to 0,
1 N 1 THR N 1 -0.31 14.0067 ; qtot -0.31
2 H 1 THR H 1 0.31 1.008 ; qtot 0,
keeping the rest as the same, and executed the command pdb2gmx and
selected the same force field and 1 and 1 for n-terminus and
c-terminus, and now there were no errors as under:
Now there are 294 residues with 3047 atoms
Warning: Long Bond (14-16 = 0.65447 nm)
Warning: Long Bond (1977-1979 = 4.21722 nm)
Warning: Long Bond (2052-2054 = 3.24295 nm)
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Number of bonds was 3113, now 3108
Generating angles, dihedrals and pairs...
Before cleaning: 4938 pairs
Before cleaning: 6118 dihedrals
There are 1565 dihedrals, 1646 impropers, 4562 angles
4938 pairs, 3108 bonds and 0 virtual sites
Total mass 33592.608 a.m.u.
Total charge 13.000 e
but, when i saw the topology file , the same number of atoms are
present and no change in the qtot...
Why is it that qtot of 13 and the increased number of atoms are not
shown in the toplogy file and whether have i selected the wrong
options or is it the wrong way of correcting the toplogy file...
On Tue, Sep 29, 2009 at 8:09 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
>> ATOM 4804 OXT PRO A 355 -53.907 34.064 13.899 1.00110.00
>> 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
>> 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
>> 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
>> 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.
>> and selected choose the "Gromos96 53a6" parameter and "none" options
>> On Tue, Sep 29, 2009 at 7:04 PM, Justin A. Lemkul <jalemkul at vt.edu> 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.
>>>> gmx-users mailing list gmx-users at gromacs.org
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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
>>> gmx-users mailing list gmx-users at gromacs.org
>>> Please search the archive at http://www.gromacs.org/search before
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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