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

Date: Fri, 19 Mar 2004 02:20:16 -0500 (EST)

Hi Amber Members,

I have a couple of question about RESP calculation. I found the .pdb

file of a Cytosine molecule in Cambridge Crystalographic Database,

CYTIDI10. I want to find the RESP charges of this particular molecule and

have a couple of questions to ask:

1. I have tried to use the program RED written by Mr. Dupradeau. I entered

the .pdb file and it took 3 days and still didnt end up with the

calculation. I killed the job. Are the gaussian calculations taking

that long? I did not change the ATOM NAMES, and later I realized that in

the sugar molecule, there is a CH2 term. Is it possible that this is the

reason for this problem? (If it is a problem for the gaussian to calculate

a particular job more than 3 days)

2. Do we have to optimize the structure of a particular molecule in order

to calculate the RESP charges? For instance, can I just use the crystal

structure I got from the CCD and just do the MEP calculation and then the

RESP calculations? Is this legitimate?

3. In the RED program, it is talking about re-orientation. I followed the

manual, and did not understand exactly what it is meant by reorientation.

In the tutorials there are examples for re-orientation, but after getting

an optimized structure, why do we have to reorient the structure? The

structure has a clear structure when viewed in InsightII or Molden. So,

isnt it legitimate to do the MEP calculation in Gaussian and then the RESP

calculations without reorient the structure?

4. I tried to follow Cornell's paper to recalculate the results published

in 1995. I read the RESP documents that are in the scripps website, and in

those info files it is saying that in order the results to be compatible

with Cornell et al. 95 force field,

#P MP2/6-31G* pop=mk iop(6/33=2)

needs to be used in the gaussian input file. I use one of the cytosine

molecule used in Cornell et al. 95 paper. The gaussian gives an error

while doing the calculations. I do not exactly remember what the error

sentence is, but it needs more space in the harddrive, more than 20 Gbyte

space. Is this normal? It happened to me twice. I used

#P HF/6-31G* pop=mk iop(6/33=2) SCF(Conver=6) Nosymm Test

which I found in Mr. Dubradeau's RED program manual, and it gives me a

result without any error.

PS: The above Gaussian command was described in an email sent by Jim

Caldwell to amber.cg1.ucsf.edu in Feb 21, 1996 with a subject "esp to

resp".

Thanks in advance.

Best,

Date: Fri, 19 Mar 2004 02:20:16 -0500 (EST)

Hi Amber Members,

I have a couple of question about RESP calculation. I found the .pdb

file of a Cytosine molecule in Cambridge Crystalographic Database,

CYTIDI10. I want to find the RESP charges of this particular molecule and

have a couple of questions to ask:

1. I have tried to use the program RED written by Mr. Dupradeau. I entered

the .pdb file and it took 3 days and still didnt end up with the

calculation. I killed the job. Are the gaussian calculations taking

that long? I did not change the ATOM NAMES, and later I realized that in

the sugar molecule, there is a CH2 term. Is it possible that this is the

reason for this problem? (If it is a problem for the gaussian to calculate

a particular job more than 3 days)

2. Do we have to optimize the structure of a particular molecule in order

to calculate the RESP charges? For instance, can I just use the crystal

structure I got from the CCD and just do the MEP calculation and then the

RESP calculations? Is this legitimate?

3. In the RED program, it is talking about re-orientation. I followed the

manual, and did not understand exactly what it is meant by reorientation.

In the tutorials there are examples for re-orientation, but after getting

an optimized structure, why do we have to reorient the structure? The

structure has a clear structure when viewed in InsightII or Molden. So,

isnt it legitimate to do the MEP calculation in Gaussian and then the RESP

calculations without reorient the structure?

4. I tried to follow Cornell's paper to recalculate the results published

in 1995. I read the RESP documents that are in the scripps website, and in

those info files it is saying that in order the results to be compatible

with Cornell et al. 95 force field,

#P MP2/6-31G* pop=mk iop(6/33=2)

needs to be used in the gaussian input file. I use one of the cytosine

molecule used in Cornell et al. 95 paper. The gaussian gives an error

while doing the calculations. I do not exactly remember what the error

sentence is, but it needs more space in the harddrive, more than 20 Gbyte

space. Is this normal? It happened to me twice. I used

#P HF/6-31G* pop=mk iop(6/33=2) SCF(Conver=6) Nosymm Test

which I found in Mr. Dubradeau's RED program manual, and it gives me a

result without any error.

PS: The above Gaussian command was described in an email sent by Jim

Caldwell to amber.cg1.ucsf.edu in Feb 21, 1996 with a subject "esp to

resp".

Thanks in advance.

Best,

-- 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 Fri Mar 19 2004 - 07:53:00 PST

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