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From: Ilyas Yildirim <yildirim.pas.rochester.edu>

Date: Mon, 19 Apr 2004 16:35:45 -0400 (EDT)

Hi Amberlist members,

I asked this question before, but did not get any answer yet. Let us say

that we have a crystal structure from pdb.org or from Cambridge

Crystallografic Database and let us say that this is just a nucleotide.

And we want to find the ESP Data points, namely we want to do MEP

calculations using Gaussian 98, and use the results in AMBER to get the

RESP charges. Is this possible to do? I am using the following command in

the gaussian input file (PS: I got this command from antechamber while

converting the pdb file into a gaussian input file)

#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt

but it gave the following error in the output

---------------------------

....

30 O nan nan nan nan nan

26 27 28 29 30

26 O nan

27 O nan nan

28 O nan nan nan

29 O nan nan nan nan

30 O nan nan nan nan nan

This structure is nearly, but not quite of a higher symmetry.

Consider Symm=Loose if the higher symmetry is desired.

Stoichiometry C9H13N3O5

Framework group C1[X(C9H13N3O5)]

Deg. of freedom 84

Full point group C1 NOp 1

Omega: Change in point group or standard orientation.

Error termination via Lnk1e in /opt/gaussian/g98/l202.exe.

Job cpu time: 1 days 1 hours 28 minutes 54.0 seconds.

File lengths (MBytes): RWF= 50 Int= 0 D2E= 0 Chk= 9 Scr= 1

---------------------------

I used molden to see how the structure looks like, but it does not look

like a normal structure.The atoms lay down on a plane which is wrong. It

seems that gaussian is trying to optimize the structure. My first question

is

1. How can I modify the input command line so that I can follow the

procedure described in Amber 7 Manual, pp. 259?

PS: I used

$ antechamber -i <inputfile>.pdb -fi pdb -o <outputfile>.com -fo gcrt

to create the Gaussian input file.

2. How can I modify the input command line so that I do not OPTIMIZE the

structure, but just get the ESP Data points?

3. Is it possible to use ANTECHAMBER if I know the ESP Data points for a

particular structure?

PS: I know that it should be possible, but I have done some MEP

calculations and I could not use ANTECHAMBER. I am assuming that the

gaussian input command I used to do MEP calculations was the reason.

Therefore, the 2nd question above is my main concern.

Thanks in advance,

Date: Mon, 19 Apr 2004 16:35:45 -0400 (EDT)

Hi Amberlist members,

I asked this question before, but did not get any answer yet. Let us say

that we have a crystal structure from pdb.org or from Cambridge

Crystallografic Database and let us say that this is just a nucleotide.

And we want to find the ESP Data points, namely we want to do MEP

calculations using Gaussian 98, and use the results in AMBER to get the

RESP charges. Is this possible to do? I am using the following command in

the gaussian input file (PS: I got this command from antechamber while

converting the pdb file into a gaussian input file)

#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt

but it gave the following error in the output

---------------------------

....

30 O nan nan nan nan nan

26 27 28 29 30

26 O nan

27 O nan nan

28 O nan nan nan

29 O nan nan nan nan

30 O nan nan nan nan nan

This structure is nearly, but not quite of a higher symmetry.

Consider Symm=Loose if the higher symmetry is desired.

Stoichiometry C9H13N3O5

Framework group C1[X(C9H13N3O5)]

Deg. of freedom 84

Full point group C1 NOp 1

Omega: Change in point group or standard orientation.

Error termination via Lnk1e in /opt/gaussian/g98/l202.exe.

Job cpu time: 1 days 1 hours 28 minutes 54.0 seconds.

File lengths (MBytes): RWF= 50 Int= 0 D2E= 0 Chk= 9 Scr= 1

---------------------------

I used molden to see how the structure looks like, but it does not look

like a normal structure.The atoms lay down on a plane which is wrong. It

seems that gaussian is trying to optimize the structure. My first question

is

1. How can I modify the input command line so that I can follow the

procedure described in Amber 7 Manual, pp. 259?

PS: I used

$ antechamber -i <inputfile>.pdb -fi pdb -o <outputfile>.com -fo gcrt

to create the Gaussian input file.

2. How can I modify the input command line so that I do not OPTIMIZE the

structure, but just get the ESP Data points?

3. Is it possible to use ANTECHAMBER if I know the ESP Data points for a

particular structure?

PS: I know that it should be possible, but I have done some MEP

calculations and I could not use ANTECHAMBER. I am assuming that the

gaussian input command I used to do MEP calculations was the reason.

Therefore, the 2nd question above is my main concern.

Thanks in advance,

-- Ilyas Yildirim --------------------------------------------------------------- - Department of Chemisty - Home Address: - - University of Rochester - - - Hutchison Hall, Office B10 - 60 Crittenden Blvd. Apt. 232 - - Rochester, NY 14627-0216 - Rochester, NY 14620 - - Ph.:(585) 275 20 31 (Office) - Ph.:(585) 242 91 37 (Home) - - Homepage: http://www.pas.rochester.edu/~yildirim/ - --------------------------------------------------------------- ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Mon Apr 19 2004 - 21:53:00 PDT

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